NAME

       psa - biological sequence alignment file format

DESCRIPTION

       psa  is  an output format used by the pftools package to describe alignments between biological sequences
       (DNA or protein) and PROSITE profiles.

       psa is apparented to the widely used biological sequence file format fasta.   Nevertheless  it  does  not
       only describe a biological sequence, it is especially used to include information of alignments between a
       motif descriptor like a PROSITE profile and a given sequence. This information is included in the  header
       and reflected in the structure of the sequence following the header line.

SYNTAX

       Each sequence in a psa alignment file or output must be preceded by a fasta header line.
       The general syntax of such a fasta header line is as follows:

              >seq_id [ free_text ]

       The  header must start with a '>' character which is directly followed by the seq_id field. This field is
       interpreted by most programs as the sequence's identifier and/or accession number. It ends at  the  first
       encountered whitespace character.
       The  pftools  programs  will  use  the  free_text  to add information about the match score, position and
       description of the sequence or motif.  Please refer to the man page of  the  corresponding  programs  for
       further information about the output formats.
       The  header  can  only  extend  over  one  line. The following lines up to a new line starting with a '>'
       character or the end of the file are interpreted as sequence data.

       The line following the header, starts the alignment data between a sequence and a PROSITE  profile.  This
       data can span over several lines of different length.
       The  data  is  formed  by  upper  or lower-case characters of the corresponding sequence alphabet (DNA or
       protein).  The gap characters '.' and '-' are also supported.
       The alignment always has at least the length of the matching profile. Insertions  or  deletions  detected
       during the motif/sequence alignment step will vary the length of the data reported, and can be identified
       using the following conventions:

              upper-case character
                     Any upper-case character of the sequence alphabet identifies a match position  between  the
                     sequence and the motif descriptor.

              lower-case character
                     A  lower-case  character  of the sequence alphabet is used to symbolize an insertion in the
                     sequence compared to the motif descriptor.

              '-' (dash) character
                     A '-' character in the output identifies  the  presence  of  a  deletion  in  the  sequence
                     compared to the motif descriptor.

EXAMPLES

       (1)    >YD28_SCHPO 556 pos. 291 - 332 sp|Q10256|YD28_SCHPO

              PTDPGlnsKIAQLVSMGFDPLEAAQALDAANGDLDVAASFLL--
              This is an example of the output produced by pfsearch(1) using the '-x' (i.e.  psa output) option.
              The first line starting with the '>' character is the fasta header. It also  contains  information
              about the raw score of the alignment as well as its position in the input sequence.
              On  the  next line you find the alignment proper. Starting at position 6, we can find an insertion
              of the 'lns' residues in the sequence compared to the motif. The last two positions of  the  motif
              are not present in the sequence (i.e. they are deleted).  This is indicated by the presence of two
              '-' (dash) characters at the end of the alignment.

NOTES

       (1)    The xpsa(5) format defines a more strict syntax of the  header  line,  allowing  the  exchange  of
              information between different sequence analysis tools. It uses keyword=value pairs to annotate the
              current match between a sequence and a motif descriptor. This syntax  can  be  easily  parsed  and
              extended, according to the needs of bioinformatic tools.

       (2)    The current implementation of the pftools package does not use the '.'  (dot) character in the psa
              output. Nevertheless psa2msa(1) will read it and interpret it in the same manner as the '-' (dash)
              character.

SEE ALSO

       xpsa(5), pfsearch(1), pfscan(1), pfw(1), pfmake(1), psa2msa(1)

AUTHOR

       This manual page was originally written by Volker Flegel.
       The pftools package was developed by Philipp Bucher.
       Any comments or suggestions should be addressed to <pftools@sib.swiss>.