sequence-file



NAME

     sequence-file - file format used for DNA,  RNA  and  protein
     sequences.


DESCRIPTION

     The general sequence file format is as follows:

          >title1
          sequence1
          >title2
          sequence2
           .
           .
           .
          >title-n
          sequence-n

     Each sequence is preceded by a one-line  descriptive  title,
     and is terminated with the next sequence.  The contents of
     the title line are ignored by most programs.  If a file con-
     tains  only  one  sequence,  the  final  two slashes are not
     required.  Sequences may contain spaces, newlines, and other
     whitespace  to improve their readability; these are not con-
     sidered part of the sequence.  Any other characters  appear-
     ing in the sequence (i.e., any printable characters) will be
     treated as part of the sequence.

     Alternatively, the Pearson/FASTA sequence file format may be
     used.   If  the  first non-blank character in a file is `>',
     the entire file is assumed to be  in  the  Pearson  sequence
     file  format.   This  should be useful for those who already
     have sequences stored for use with FASTA.  The first line is
     treated  as  the name of the sequence; the sequence follows,
     with  whitespace  ignored.   The  sequence  terminates  when
     another `>' character is read or end-of-file is encountered.


SEE ALSO

     seqaln-intro(1), globalS(1), mglobalS(1), globalD(1),<
/STRONG>  mglo-
     balD(1),  fitS(1),  mfitS(1),  pfitS(1),  fitD(1)
, mfitD(1),
     overS(1),  moverS(1),  localS(1),  mlocalS(1),  srlocalS(1),
     msrlocalS(1), trlocalS(1), mtrlocalS(1), pvlocalS(1),<
/STRONG> mpvlo-
     calS(1).