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glam2 - Gapped Local Alignment of Motifs

GLAM2(1) glam2 Manual 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.
The source code and the documentation of GLAM2 are released in the public domain.
 
05/19/2008 GLAM2 1056