.TH PSA2MSA 1 "June 1999" "pftools 2.2"
.SH NAME
psa2msa \-  reformat PSA file to Pearson/Fasta multiple sequence alignment file 
.SH SYNOPSIS
.B psa2msa 
[ -dlpu ] [ [ psa-file | - ] ]   [ M=#]
.SH DESCRIPTION
.B 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. 
.I psa-file
contains alignments of several sequence segments to the same profile 
in PSA format. 
Such a file is typically generated by program 
.B pfsearch  
using option
.I -x.
The output can be converted into other formats (
.I e.g. 
MSF) with the aid of the public domain
program
.B readseq
(available from ftp.bio.indiana.edu:/molbio/readseq). 
.B psa2msa
can be used as a filter if - is used instead of the input
filename, or if the input filename is omitted. 
.SH OPTIONS
.TP
\-d
Replace periods by dashes on output.
.TP
\-l
Replace upper case letters by lower case letters on output.
.TP
\-p
Replace dashes by periods on output.
.TP
\-u
Replace lower case letters by upper case letters on output.
.SH PARAMETERS
.TP
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. 
.I 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. 
.SH EXAMPLES
.TP
(1)
.B pfsearch
-bx ecp.prf CVPBR322 | 
.B psa2msa
-du |
.B readseq
-p -fMSF > ecp.msf

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

.I See
also manual pages of
.B pfsearch. 
.SH AUTHOR
Philipp Bucher
.br
Philipp.Bucher@isrec.unil.ch