SYNOPSIS
- glam2scan [options] alphabet my_motif.glam2 my_seqs.fa
DESCRIPTION
glam2scan finds matches, in a sequence database, to a motif discovered by glam2. Each match receives a score, indicating how well it fits the motif.
OPTIONS (DEFAULT SETTINGS)
-h
- Show all options and their default settings.
-o
- Output file (stdout).
-n
- Number of alignments to report (25).
-2
- Examine both strands - forward and reverse complement.
-D
- Deletion pseudocount (0.1).
-E
- No-deletion pseudocount (2.0).
-I
- Insertion pseudocount (0.02).
-J
- No-insertion pseudocount (1.0).
-d
- Dirichlet mixture file.
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 <[email protected]>
- 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.