man glam2scan (1): finds a GLAM2 motif in a database

SYNOPSIS

glam2scan [options] alphabet my_motif.glam2 my_seqs.fa

An alphabet other than p or n is interpreted as the name of an alphabet file.

DESCRIPTION

glam2scan finds matches, in a sequence database, to a motif discovered by glam2. Each match receives a score, indicating how well it fits the motif.

OPTIONS (DEFAULT SETTINGS)

-h

: Show all options and their default settings.

-o

: Output file (stdout).

-n

: Number of alignments to report (25).

-2

: Examine both strands - forward and reverse complement.

-D

: Deletion pseudocount (0.1).

-E

: No-deletion pseudocount (2.0).

-I

: Insertion pseudocount (0.02).

-J

: No-insertion pseudocount (1.0).

-d

: Dirichlet mixture file.

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.