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.