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.