Provided by: pftools_3+dfsg-2build1_amd64 
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