table of contents
GLAM2(1) | glam2 Manual | GLAM2(1) |
NAME¶
glam2 - Gapped Local Alignment of MotifsSYNOPSIS¶
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)¶
-hShow 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.05/19/2008 | GLAM2 1056 |