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.