.\"     Title: GLAM2-PURGE
.\"    Author: Andrew Neuwald
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
.\"      Date: 05/19/2008
.\"    Manual: glam2 Manual
.\"    Source: GLAM2 1056
.\"
.TH "GLAM2\-PURGE" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
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.nh
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.SH "NAME"
glam2-purge \- Removes redundant sequences from a FASTA file
.SH "SYNOPSIS"
.HP 12
\fBglam2\-purge\fR \fIfile\fR \fBscore\fR [\fBoptions\fR]
.SH "DESCRIPTION"
.PP

\fBglam2\-purge\fR
is a modified version of Andrew Neuwald\'s
\fBpurge\fR
program that removes redundant sequences from a FASTA file\&. This is recommended in order to prevent highly similar sequences distorting the search for motifs\&. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user\&. The output file is named <file>\&.<score>\&. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/\-1 scoring scheme for DNA\&. Purge can also be used to mask tandem repeats\&. It uses the XNU program for this purpose\&.
.SH "OPTIONS"
.PP
\fB\-n\fR
.RS 4
Sequences are DNA (default: protein)\&.
.RE
.PP
\fB\-b\fR
.RS 4
Use blast heuristic method (default for protein)\&.
.RE
.PP
\fB\-e\fR
.RS 4
Use an exhaustive method (default for DNA)\&.
.RE
.PP
\fB\-q\fR
.RS 4
Keep first sequence in the set\&.
.RE
.PP
\fB\-x\fR
.RS 4
Use xnu to mask protein tandem repeats\&.
.RE
.SH "SEE ALSO"
.PP
\fBglam2\fR(1),
\fBglam2format\fR(1),
\fBglam2mask\fR(1),
\fBglam2scan\fR(1),
\fBxnu\fR(1)
.PP
The full Hypertext documentation of GLAM2 is available online at
\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
or on this computer in
\fI/usr/share/doc/glam2/\fR\&.
.SH "REFERENCES"
.PP
Purge was written by Andy Neuwald and is described in more detail in Neuwald et al\&., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618\(en1632, 1995\&. Please cite it if you use Purge\&.
.PP
If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
.SH "AUTHORS"
.PP
\fBAndrew Neuwald\fR
.sp -1n
.IP "" 4
Author of purge, renamed glam2\-purge in Debian\&.
.PP
\fBMartin Frith\fR
.sp -1n
.IP "" 4
Modified purge to be ANSI standard C and improved the user interface\&.
.PP
\fBTimothy Bailey\fR
.sp -1n
.IP "" 4
Modified purge to be ANSI standard C and improved the user interface\&.
.PP
\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
.sp -1n
.IP "" 4
Formatted this manpage in DocBook XML for the Debian distribution\&.
.SH "COPYRIGHT"
.PP
The source code and the documentation of Purge and GLAM2 are released in the public domain\&.
.sp