NAME

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

SYNOPSIS

       psa2msa   [ -dhlpu ] [ -M insert_len ] [ -W width ] [ psa_file | - ] [ parameters ]

DESCRIPTION

       psa2msa reformats a psa(5) 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(5)
       format. Such a file is typically generated by the programs pfsearch(1) or pfscan(1)  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://ftp.bio.indiana.edu/molbio/readseq) or
       used  directly  with  pfmake(1) or pfw(1).  If '-' is specified instead of a filename, the
       psa(5) alignment is read from the standard input.

OPTIONS

       psa_file
              Input multiple sequence alignment.
              The content of the file must be in psa(5) format.  If the filename is replaced by a
              '-', psa2msa will read the input alignment from stdin.

       -d     Replace periods '.'  by dashes '-' on output.

       -h     Display usage help text.

       -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.

       -M insert_len
              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.   A  negative  value  of
              'insert_len' means no upper limit for the length of an insertion (i.e.  no residues
              will be deleted from an insertion).  If 'insert_len' is zero, all insert  positions
              will  be  removed.   Setting  an insertion length limit helps to keep the resulting
              alignment at manageable size.
              Type: integer
              Default: -1

              Note:  The meaning of the value '0' for this parameter has been changed compared to
                     version 2.2 of the pftools package.

       -W width
              Set alignment output width.
              The value of 'width' specifies how many residues will be output on one line.
              Type: integer
              Default: 60

PARAMETERS

       Note:  for  backwards  compatibility,  release  2.3  of the pftools package will parse the
              version 2.2 style parameters, but these are deprecated and the corresponding option
              (refer to the options section) should be used instead.

       M=#    Maximal insertion length
              Use option -M instead.

       W=#    Output width.
              Use option -W instead.

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.  The file 'ecp.prf'  contains  a  profile  for  E.  coli
              promoters.  The file 'CVPBR322' contains EMBL entry J01749|CVPBR322.  The result in
              'ecp.msf' can further be processed by GCG programs accepting MSF files as input.

EXIT CODE

       On successful completion of its task, psa2msa will return an exit code of 0. If  an  error
       occurs,  a  diagnostic  message will be output on standard error and the exit code will be
       different from 0. When conflicting options where passed to the program but the task  could
       nevertheless be completed, warnings will be issued on standard error.

SEE ALSO

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

AUTHOR

       The pftools package was developed by Philipp Bucher.
       Any comments or suggestions should be addressed to <pftools@sib.swiss>.