GLAM2(1)
NAME
glam2 - Gapped Local Alignment of Motifs
SYNOPSIS
glam2 [options] alphabet my_seqs.fa An alphabet other than p or n is interpreted as the name of an alphabet file.
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).
SEE ALSO
glam2format(1), glam2mask(1), glam2-purge(1), glam2scan(1)
The full Hypertext documentation of GLAM2 is available online at
http://bioinformatics.org.au/glam2/ or on this computer in
/usr/share/doc/glam2/.
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 <plessy@debian.org>
- 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.