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>.

pftools 2.3                                        August 2003                                        PSA2MSA(1)