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GLAM2SCAN(1) glam2 Manual GLAM2SCAN(1)

NAME

glam2scan - 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.

SEE ALSO

glam2format(1), glam2mask(1), glam2-purge(1), glam2(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.
 
05/19/2008 GLAM2 1056