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<?xml version="1.0" encoding="utf-8"?>
<!-- XML Authors: Bertrand Néron -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
<tutorial>
<head>
<name>Sequences_formats</name>
<version>1.0</version>
<doc>
<title>Sequences formats</title>
<description>
<text lang="en">common used formats for sequences</text>
</description>
<authors>N. Joly</authors>
</doc>
<category>data formats</category>
<interface type="tutorial">
<div xmlns="http://www.w3.org/1999/xhtml">
<p>This document illustrates some common formats used for sequences representation.</p>
<dl>
<dt>
<strong>
<a name="embl" class="item">
<strong>EMBL</strong>
</a>
</strong>
</dt>
<dd>
<pre>
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
//
</pre>
</dd>
<dt>
<strong>
<a name="fasta" class="item">
<strong>FASTA</strong>
</a>
</strong>
</dt>
<dd>
<pre>
>MMVASPHOS
ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
ccgccctccgcgcagccatg
</pre>
</dd>
<dt>
<strong>
<a name="gcg" class="item">
<strong>GCG</strong>
</a>
</strong>
</dt>
<dd>
<pre>
!!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
</pre>
</dd>
<dt>
<strong>
<a name="gde" class="item">
<strong>GDE</strong>
</a>
</strong>
</dt>
<dd>
<pre>
#sample1
TTCAAGAGAAACAGCGGCCAAGGAAAAGACTCGGCATGATTGTCCATAGCTTACAAAGCG
#sample2
TTCAAGAGAAACAGCGGCTGGGGGAAAGACTCGTCCTGATTGCCTGTAGATGGTAAAGCG
</pre>
</dd>
<dt>
<strong>
<a name="genbank" class="item">
<strong>GENBANK</strong>
</a>
</strong>
</dt>
<dd>
<pre>
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
//
</pre>
</dd>
<dt>
<strong>
<a name="ig" class="item">
<strong>IG</strong>
</a>
</strong>
</dt>
<dd>
<pre>
; comment
U03518
AACCTGCGGAAGGATCATTACCGAGTGCGGGTCCTTTGGGCCCAACCTCCCATCCGTGTC
TATTGTACCCTGTTGCTTCGGCGGGCCCGCCGCTTGTCGGCCGCCGGGGGGGCGCCTCTG
TGAGTTGATTGAATGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGC1
</pre>
</dd>
<dt>
<strong>
<a name="nbrf" class="item">
<strong>NBRF</strong>
</a>
</strong>
</dt>
<dd>
<pre>
>P1;CCHU
cytochrome c [validated] - human
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
</pre>
</dd>
<dt>
<strong>
<a name="nbrf" class="item">
<strong>NBRF (pir)</strong>
</a>
</strong>
</dt>
<dd>
<pre>
>P1;CCHU
cytochrome c [validated] - human
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
</pre>
</dd>
<dt>
<strong>
<a name="codata" class="item">
<strong>CODATA</strong>
</a>
</strong>
</dt>
<dd>
<pre>
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
///
</pre>
</dd>
<dt>
<strong>
<a name="raw" class="item">
<strong>RAW</strong>
</a>
</strong>
</dt>
<dd>
<pre>
ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
ccgccctccgcgcagccatg
</pre>
<p>
<strong>Warning</strong>
: This format cannot handle more than one sequence per file.
</p>
</dd>
<dt>
<strong>
<a name="swissprot" class="item">
<strong>SWISSPROT</strong>
</a>
</strong>
</dt>
<dd>
<pre>
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
//
</pre>
</dd>
</dl>
</div>
</interface>
</head>
</tutorial>
|
