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

pftools 2.2                                         June 1999                                         PSA2MSA(1)