glam2mask [options] <glam2 motif> <sequence file>
This program masks the occurrences of a GLAM2 motif 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.
The name of a GLAM2 output file.
The name of a file containing FASTA formatted sequences.
The input sequences are output with the GLAM2 motif sites masked out with 'x's. The sequences are normally sent to standard output but this can be changed by specifying the -o option.
|-o||output file||The masked sequences are written to output file.||The masked sequences are written to standard output.|
|-x||mask character||The instances of the glam2 motif are masked out with the mask character.||The instances of the glam2 motif are masked out with 'x'.|
glam2mask -o mask1.fa my_motif.glam2 my_seqs.fa
glam2mask -x n my_motif.glam2 my_seqs.fa