glam21
Gapped local alignment of motifs
Usage
glam2 [options]
alphabet
my_seqs.fa
Overview
GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs.
Options (default settings)
-h
Show all options and their default settings.
-o
Output file (stdout).
-r
Number of alignment runs (10).
-n
End each run after this many iterations without improvement (10000).
-2
Examine both strands - forward and reverse complement.
-z
Minimum number of sequences in the alignment (2).
-a
Minimum number of aligned columns (2).
-b
Maximum number of aligned columns (50).
-w
Initial number of aligned columns (20).
-d
Dirichlet mixture file.
-D
Deletion pseudocount (0.1).
-E
No-deletion pseudocount (2.0).
-I
Insertion pseudocount (0.02).
-J
No-insertion pseudocount (1.0).
-q
Weight for generic versus sequence-set-specific residue abundances (1e+99).
-t
Initial temperature (1.2).
-c
Cooling factor per n iterations (1.44).
-u
Temperature lower bound (0.1).
-p
Print progress information at each iteration.
-m
Column-sampling moves per site-sampling move (1.0).
-x
Site sampling algorithm: 0=FAST 1=SLOW 2=FFT (0).
-s
Seed for pseudo-random numbers (1).
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).