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glam2mask - masks a GLAM2 motif in sequences

GLAM2MASK(1) glam2 Manual 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.
The source code and the documentation of GLAM2 are released in the public domain.
 
05/19/2008 GLAM2 1056