glam2(1) 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).

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 <[email protected]>

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.