SYNOPSIS
- glam2 [options] alphabet my_seqs.fa
DESCRIPTION
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).
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.