glam2format1
Converts glam2 motifs to fasta or msf format
Usage
glam2format [options]
my_format
my_motif.glam2
Overview
glam2format reads in a motif found by glam2, and writes it in a standard alignment format (FASTA-with-gaps or MSF). This enables the alignment to be passed to third-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo. On the other hand, not all the motif information is preserved: in particular, the key positions are lost. Only the top motif in glam2 output is converted.
Options (default settings)
-o
Output file (stdout).
-c
Make a compact alignment. By default, residues that are inserted between key positions are written as unaligned with each other. This best reflects glam2´s intention, but it can make the alignment large and full of gaps. With -c, inserted residues are written as arbitrarily aligned with each other, just as they appear in the glam2 output.
-f
Sequence file to make a “global” alignment by adding flanking sequences from the original FASTA-format sequence file. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the -c option. The sequences should have unique names and their order should be unchanged.
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).
Releases
Unchanged in 9 releases since Debian 5.0 (Lenny).