.TH PFSEARCH "1" "March 2017" "pfsearch 3" "User Commands"
.SH NAME
pfsearch \- search protein and DNA generalized profiles (legacy)
.SH SYNOPSIS
.B pfsearch
[ \fI\,-abCdfhlLmMkrsuvWxyz \/\fR] [ \fI\,profile-file | - \/\fR] [ \fI\,seq-library-file | - \/\fR] [ \fI\,parameters \/\fR]
.SH DESCRIPTION
Build protein and DNA generalized profiles and use them to scan and align sequences,
and search databases.
.SH OPTIONS
.HP
\fB\-a\fR: report optimal alignment for all sequences.
.HP
\fB\-b\fR: search complementary strand of DNA sequences.
.HP
\fB\-f\fR: input sequence file is in FASTA format.
.HP
\fB\-h\fR: print usage help text.
.HP
\fB\-l\fR: indicate highest cut\-off level (number).
.HP
\fB\-L\fR: indicate highest cut\-off level (text).
.HP
\fB\-m\fR: report individual matches for circular profiles.
.HP
\fB\-r\fR: use raw score.
.HP
\fB\-u\fR: force profile disjointness to UNIQUE.
.HP
\fB\-C\fR<value>:
.IP
cut\-off value. An integer value forces \fB\-r\fR. Same as parameter C.
.HP
\fB\-M\fR<value>:
.IP
set the normalization mode to use for the score computation.
Overrides the profile PRIORITY parameter.
.IP
output modifiers:
.HP
\fB\-d\fR: impose length limit on sequence description.
.HP
\fB\-k\fR: output using the xPSA header (using keyword=value pairs).
.HP
\fB\-s\fR: list sequences of the matched regions.
.HP
\fB\-v\fR: suppress warnings on stderr.
.HP
\fB\-x\fR: list alignments in PSA format.
.HP
\fB\-y\fR: list alignments in human readable form.
.HP
\fB\-z\fR: indicate profile start and stop positions.
.HP
\fB\-W\fR<value>:
.IP
specifies the output width. Same as parameter W.
.IP
valid (but deprecated) parameters are:
.TP
[C=cut\-off\-value]
use option \fB\-C\fR instead
.TP
[W=output\-width]
use option \fB\-W\fR instead
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.