GLAM2MASK(1)
NAME
glam2mask - masks a GLAM2 motif in sequences
SYNOPSIS
glam2mask [options] my_motif.glam2 my_seqs.fa
DESCRIPTION
glam2mask masks a glam2 motif out of sequences, so that weaker motifs
can be found. Masking replaces residues aligned to key positions with
the symbol 'x'. By alternately applying glam2 and glam2mask several
times, it is possible to find the strongest, second-strongest,
third-strongest, etc. motifs in a set of sequences.
OPTIONS (DEFAULT SETTINGS)
- -o
- Output file (stdout).
- -x
- Mask character (x).
SEE ALSO
glam2format(1), glam2(1), glam2-purge(1), glam2scan(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/.
REFERENCE
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
- Martin Frith
- Author of GLAM2.
- Timothy Bailey
- Author of GLAM2.
- Charles Plessy <plessy@debian.org>
- Formatted this manpage in DocBook XML for the Debian distribution.
COPYRIGHT
- The source code and the documentation of GLAM2 are released in the
public domain.