SEQFMT(1)

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.