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.