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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.