NAME
glam2-purge - Removes redundant sequences from a FASTA file
SYNOPSIS
glam2-purge file score [options]
DESCRIPTION
glam2-purge is a modified version of Andrew Neuwald´s purge 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.
OPTIONS
-n
Sequences are DNA (default: protein).
-b
Use blast heuristic method (default for protein).
-e
Use an exhaustive method (default for DNA).
-q
Keep first sequence in the set.
-x
Use xnu to mask protein tandem repeats.
SEE ALSO
glam2(1), glam2format(1), glam2mask(1), glam2scan(1), xnu(1)
The full Hypertext documentation of GLAM2 is available online at
http://bioinformatics.org.au/glam2/ or on this computer in
/usr/share/doc/glam2/.
REFERENCES
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, 4:1618–1632, 1995. Please
cite it if you use Purge.
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).
AUTHORS
Andrew Neuwald
Author of purge, renamed glam2-purge in Debian.
Martin Frith
Modified purge to be ANSI standard C and improved the user
interface.
Timothy Bailey
Modified purge to be ANSI standard C and improved the user
interface.
Charles Plessy <plessy@debian.org>
Formatted this manpage in DocBook XML for the Debian distribution.
COPYRIGHT
The source code and the documentation of Purge and GLAM2 are released
in the public domain.