glam2 − Gapped Local Alignment of Motifs
glam2 [options] alphabet my_seqs.fa |
An alphabet other than p or n is interpreted as the name of an alphabet file.
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.
−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).
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/.
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).
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.