NAME

       psa2msa -  reformat PSA file to Pearson/Fasta multiple sequence alignment file

SYNOPSIS

       psa2msa [ -dlpu ] [ [ psa-file | - ] ]   [ M=#]

DESCRIPTION

       psa2msa  reformats  a  PSA-formatted profile-sequence alignment file into a Pearson/Fasta-
       formatted multiple sequence alignment file.  The result is written to the standard output.
       psa-file  contains  alignments  of  several  sequence  segments to the same profile in PSA
       format.  Such a file is typically generated by program  pfsearch  using  option  -x.   The
       output  can be converted into other formats ( e.g.  MSF) with the aid of the public domain
       program readseq (available from ftp.bio.indiana.edu:/molbio/readseq).  psa2msa can be used
       as  a  filter  if  -  is  used  instead of the input filename, or if the input filename is
       omitted.

OPTIONS

       -d     Replace periods by dashes on output.

       -l     Replace upper case letters by lower case letters on output.

       -p     Replace dashes by periods on output.

       -u     Replace lower case letters by upper case letters on output.

PARAMETERS

       M=#    Maximal length of an insertion.  If the real length of an  insertion  exceeds  this
              value,  the  excess  number  of  residues  will  be  deleted from the center of the
              insertion.  M=0 means no upper limit for the length of an  insertion.   Setting  an
              insertion  length  limit  helps to keep the resulting alignment at manageable size.
              Default: M=0.

EXAMPLES

       (1)    pfsearch -bx ecp.prf CVPBR322 | psa2msa -du | readseq -p -fMSF > ecp.msf

              Generates a multiple sequence alignment of predicted  E.  coli  promoters  on  both
              strands  of  plasmid  pBR322.   ecp.prf  contains  a profile for E. coli promoters.
              CVPBR322 contains EMBL entry J01749|CVPBR322.  The result in ecp.msf can further be
              processed by GCG programs accepting MSF files as input.

              See also manual pages of pfsearch.

AUTHOR

       Philipp Bucher
       Philipp.Bucher@isrec.unil.ch