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.

GLAM2 1056							    05/19/2008							      GLAM2SCAN(1)