This document illustrates some common formats used for sequences representation.
ID MMVASPHOS standard; RNA; EST; 140 BP.
AC X97897;
DE M.musculus mRNA for protein homologous to
DE vasodilator-stimulated phosphoprotein
SQ Sequence 140 BP; 25 A; 58 C; 39 G; 17 T; 1 other;
ttctcccaga agctgactct atggngaccc cgagagagac tgagcagaac 60
ccccgcaccc ctgcacttcc aatcaggggc gccccgggag cactccccgt 120
ccgccctccg cgcagccatg 140
//
>MMVASPHOS
ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
ccgccctccgcgcagccatg
!!NA_SEQUENCE 1.0
(No documentation)
dna1.txt Length: 88 Nov 22, 2001 14:38 Type: N Check: 3818 ..
1 TAGTCGTAGT CGGAGCGATG CTGACGATGA CGATGACGAT CGTAGCTGAT
51 CGATCGAGCT GATGCTGATC GAGCTAGCTG ATCGATCG
#sample1
TTCAAGAGAAACAGCGGCCAAGGAAAAGACTCGGCATGATTGTCCATAGCTTACAAAGCG
#sample2
TTCAAGAGAAACAGCGGCTGGGGGAAAGACTCGTCCTGATTGCCTGTAGATGGTAAAGCG
LOCUS HUMHBV1 130 bp DNA PRI 17-JUN-1993
DEFINITION Human DNA/endogenous Hepatitis B virus (HBV) DNA, left
host viral junction.
ACCESSION M15770
BASE COUNT 32 a 43 c 29 g 26 t
ORIGIN
1 agcgggcagt gcagctgctt ggacagcagg ggtgtttctt caacccaggc
61 ctcctgtcac aacaggccca ttcaattctg aacctgcaag ccaactccaa
121 cctcttttcc cagggggaac caaaaaccct
//
; comment
U03518
AACCTGCGGAAGGATCATTACCGAGTGCGGGTCCTTTGGGCCCAACCTCCCATCCGTGTC
TATTGTACCCTGTTGCTTCGGCGGGCCCGCCGCTTGTCGGCCGCCGGGGGGGCGCCTCTG
TGAGTTGATTGAATGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGC1
>P1;CCHU
cytochrome c [validated] - human
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
>P1;CCHU
cytochrome c [validated] - human
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
ENTRY CCHU #type complete
TITLE cytochrome c [validated] - human
ACCESSIONS A31764; A05676; I55192; A00001
SUMMARY #length 105 #molecular-weight 11749 #checksum 3247
SEQUENCE
5 10 15 20 25 30
1 M G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G
31 P N L H G L F G R K T G Q A P G Y S Y T A A N K N K G I I W
61 G E D T L M E Y L E N P K K Y I P G T K M I F V G I K K K E
91 E R A D L I A Y L K K A T N E
///
ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
ccgccctccgcgcagccatg
Warning : This format cannot handle more than one sequence per file.
ID 100K_RAT STANDARD; PRT; 149 AA.
AC Q62671;
DE 100 kDa protein (EC 6.3.2.-).
SQ SEQUENCE 149 AA; 17004 MW; D06484B8BC29112E CRC64;
MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK
PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN
SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV
//
"The name should be ten characters in length, filled out to the full ten characters by blanks if shorter. Any printable ASCII/ISO character is allowed in the name, except for parentheses ("(" and ")"), square brackets ("[" and "]"), colon (":"), semicolon (";") and comma (","). If you forget to extend the names to ten characters in length by blanks, the program will get out of synchronization with the contents of the data file, and an error message will result." (for complete description of phylip format see: http://bioweb2.pasteur.fr/docs/phylip/doc/main.html)
"One slight difference with PHYLIP format deals with sequence name lengths. While PHYLIP format limits this length to ten characters, PhyML can read up to hundred character long sequence names. Blanks and the symbols “(),:” are not allowed within sequence names"
These two formats are in some case non compliant. The program we use to detect sequences format and convert them is not able to use Phyml format, so it convert sequence in Phylip. When sequences name are longer than 10 characters the resulting file is not compliant to use with Phyml (the sequence names are truncated to 10 characters and there is no space between name and sequence). It exists a workaround to this problem.
This document illustrates some common formats used for aligned sequences representation.
CLUSTAL W (1.82) multiple sequence alignment
MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTL
MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTL
MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTL
MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------
*:** *:**:**:*:.::**:***:*::***
MALK_ECOLI LRMIAGLETITSGDLACRRLHKEPGV
MALK_SALTY LRMIAGLETITSGDLACRRLHQEPGV
MALK_ENTAE LRMIAGLETVTSGDL-----------
MALK_PHOLU LRM-----------------------
***
Warning : Names must not contain spaces or exceed 30 characters.
>MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA GLETITSGDLACRRLHKEPGV >MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA GLETITSGDLACRRLHQEPGV >MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA GLETVTSGDL----------- >MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------LRM-- ---------------------
#mega !Title Multiple Sequence Alignment;
#MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA GLETITSGDLACRRLHKEPGV #MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA GLETITSGDLACRRLHQEPGV #MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA GLETVTSGDL----------- #MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF------------------- ---------------------
!!AA_MULTIPLE_ALIGNMENT 1.0 PileUp of: @pep.list
msf.seq MSF: 55 Type: P Nov 22, 2001 11:02 Check: 2529 ..
Name: m73237 Len: 655 Check: 7493 Weight: 1.00 Name: l28824 Len: 655 Check: 5456 Weight: 1.00 Name: u04379 Len: 655 Check: 9580 Weight: 1.00
//
1 50
m73237 ~~~~~MADSA NHLPFFFGQI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
l28824 MASSGMADSA NHLPFFFGNI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
u04379 ~~~~~MPDPA AHLPFFYGSI SRAEAEEHLK LAGMADGLFL LRQCLRSLGG
51
m73237 ~~~~~
l28824 ~~~~~
u04379 AACG*
Warning : This format cannot handle more than 500 sequences in a single alignment.
#NEXUS
begin data; dimensions ntax=2 nchar=89; format datatype=Protein interleave gap=- missing='.'; matrix [ 1 50] btdDm -------AQQQQHHLHMQQAQHH-----------LHLSH------QQAQQ TSp1 --------------------AEH-----------PSLR--------GTPL
[ 51 80] btdDm YACPICSKKFSRSDHLSKHKKTHF------ TSp1 FACPICNKRFMRSDHLAKHVKTHN------
;
endblock;
Warning : Text enclosed in brackets is considered as comment, and thus ignored.
Sequential (PHYLIPS):
2 109
ATISA1 GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENNDG
ENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMGDE
YGHTKGGN---
POTISA1 GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKDG
ENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMGDE
YGHTKGGN---
Interleaved (PHYLIPI):
2 109
ATISA1 GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENND
POTISA1 GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKD
GENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMG
GENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMG
DEYGHTKGGN---
DEYGHTKGGN---
Warning : Species names may not contain characters `( ) : ; , [ ]' and exceed 10 characters.
# STOCKHOLM 1.0
MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
MALK_ECOLI RCHLFREDGTACRRLHKEPGV MALK_SALTY RCHLFREDGSACRRLHQEPGV MALK_ENTAE --------------------- MALK_PHOLU --------------------- //
You can use the portal without registering at all. This means that you are welcome as a guest. The results of your jobs will be available for a limited time, even if you exit the portal for a short while. However, you will not be able to use them if you connect from another place.
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Click on the sign-in link located on the top right of the page, then click on register. Enter your e-mail, and pick a password (this password is specific to the portal). Once submitted, you will receive an e-mail requesting your confirmation for this registration. You can then save your data, and access them from anywhere.
Welcome to Mobyle, a portal to run bioinformatics analyses. This tutorial is interactive: it helps you to open forms, navigate through the portal and fill some fields. At any time, you can come back here by clicking on the Tutorials tab above.
Let's start by running a first analysis: predict a protein membrane topology with the toppred program. Clickinghere opens the toppred form. The first field is for the protein sequence. You can paste the following data:
>sp|P02914|MALK_ECOLI MALTOSE/MALTODEXTRIN TRANSPORT ATP-BINDING PROTEIN MALK.
MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL
FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKPAGAKKEVINQRVNQVAEV
LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH
KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN
FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVIL
EGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGT
ACRRLHKEPGV
Then launch the program by clicking on the Run button.
When finished, the results are available under the Jobs tab. The output starts by some details on the job, followed by the output files. You can return to the form anytime by clicking on its tab, at the top of the page.
You can input data either by copy/paste, file loading, database fetch, or selection of the output from a previous analysis. Let us try this with some examples.
Results will be available as long as the server keeps the corresponding files. To access to the results of a previously run job, use the "Jobs" drawer on the left.
The left panel displays 4 "drawers", in order to help you navigate in the portal. The first one provides a list of the available programs, classified by bioinformatics domain. By default, all programs are listed, but you can filter this long list by providing a search term in the search for field. For instance, enter the term "matrix" - notice that you don't need to hit return to start the search. Only the program having the word "matrix" in their description will be displayed. When mousing over the name of the program, the information bullet displays the matched text.