File: seqfmt.man

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.\" ========================================================================
.\"
.IX Title "SEQFMT 5"
.TH SEQFMT 5 "2013-03-29" "Unix" "User Manuals"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
seqfmt \- Sequences formats" 4
.IX Item "seqfmt - Sequences formats"
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This document illustrates some common formats used for sequences
representation.
.IP "\fB\s-1EMBL\s0\fR" 4
.IX Item "EMBL"
.Vb 9
\& 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
\& //
.Ve
.IP "\fB\s-1FASTA\s0\fR" 4
.IX Item "FASTA"
.Vb 4
\& >MMVASPHOS
\& ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
\& ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
\& ccgccctccgcgcagccatg
.Ve
.IP "\fB\s-1GCG\s0\fR" 4
.IX Item "GCG"
.Vb 3
\& !!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
.Ve
.IP "\fB\s-1GDE\s0\fR" 4
.IX Item "GDE"
.Vb 4
\& #sample1
\& TTCAAGAGAAACAGCGGCCAAGGAAAAGACTCGGCATGATTGTCCATAGCTTACAAAGCG
\& #sample2
\& TTCAAGAGAAACAGCGGCTGGGGGAAAGACTCGTCCTGATTGCCTGTAGATGGTAAAGCG
.Ve
.IP "\fB\s-1GENBANK\s0\fR" 4
.IX Item "GENBANK"
.Vb 10
\& 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
\& //
.Ve
.IP "\fB\s-1IG\s0\fR" 4
.IX Item "IG"
.Vb 5
\& ; comment
\& U03518
\& AACCTGCGGAAGGATCATTACCGAGTGCGGGTCCTTTGGGCCCAACCTCCCATCCGTGTC
\& TATTGTACCCTGTTGCTTCGGCGGGCCCGCCGCTTGTCGGCCGCCGGGGGGGCGCCTCTG
\& TGAGTTGATTGAATGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGC1
.Ve
.IP "\fB\s-1NBRF\s0\fR (pir)" 4
.IX Item "NBRF (pir)"
.Vb 4
\& >P1;CCHU
\& cytochrome c [validated] \- human
\& MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
\& GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
.Ve
.IP "\fB\s-1CODATA\s0\fR" 4
.IX Item "CODATA"
.Vb 11
\& 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
\& ///
.Ve
.IP "\fB\s-1RAW\s0\fR" 4
.IX Item "RAW"
.Vb 3
\& ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
\& ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
\& ccgccctccgcgcagccatg
.Ve
.Sp
\&\fBWarning\fR: This format cannot handle more than one sequence per file.
.IP "\fB\s-1SWISSPROT\s0\fR" 4
.IX Item "SWISSPROT"
.Vb 8
\& 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
\& //
.Ve
.SH "SEE ALSO"
.IX Header "SEE ALSO"
.IP "\fBsquizz\fR(1), \fBalifmt\fR(5)" 4
.IX Item "squizz(1), alifmt(5)"
.SH "AUTHOR"
.IX Header "AUTHOR"
Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.