NAME

       seqfmt - Sequences formats

DESCRIPTION

       This document illustrates some common formats used for sequences representation.

       EMBL
            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
            //

       FASTA
            >MMVASPHOS
            ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
            ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
            ccgccctccgcgcagccatg

       GCG
            !!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

       GDE
            #sample1
            TTCAAGAGAAACAGCGGCCAAGGAAAAGACTCGGCATGATTGTCCATAGCTTACAAAGCG
            #sample2
            TTCAAGAGAAACAGCGGCTGGGGGAAAGACTCGTCCTGATTGCCTGTAGATGGTAAAGCG

       GENBANK
            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
            //

       IG
            ; comment
            U03518
            AACCTGCGGAAGGATCATTACCGAGTGCGGGTCCTTTGGGCCCAACCTCCCATCCGTGTC
            TATTGTACCCTGTTGCTTCGGCGGGCCCGCCGCTTGTCGGCCGCCGGGGGGGCGCCTCTG
            TGAGTTGATTGAATGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGC1

       NBRF (pir)
            >P1;CCHU
            cytochrome c [validated] - human
            MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
            GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*

       CODATA
            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
            ///

       RAW
            ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
            ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
            ccgccctccgcgcagccatg

           Warning: This format cannot handle more than one sequence per file.

       SWISSPROT
            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
            //

SEE ALSO

       squizz(1), alifmt(5)

AUTHOR

       Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.