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GLAM2

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.

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