Masks a glam2 motif in sequences
glam2mask [options] my_motif.glam2 my_seqs.fa
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.
-o
Output file (stdout).
-x
Mask character (x).
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/.
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).
Martin Frith
Author of GLAM2.
Timothy Bailey
Author of GLAM2.
Charles Plessy <[email protected]>
Formatted this manpage in DocBook XML for the Debian distribution.
The source code and the documentation of GLAM2 are released in the public domain.