Man page - glam2(1)
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Manual
GLAM2
NAMESYNOPSIS
DESCRIPTION
OPTIONS (DEFAULT SETTINGS)
SEE ALSO
REFERENCE
AUTHORS
COPYRIGHT
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>
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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.