glam2scan1
Finds a glam2 motif in a database
Usage
glam2scan [options]
alphabet
my_motif.glam2
my_seqs.fa
Overview
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).
Releases
Unchanged in 9 releases since Debian 5.0 (Lenny).