debian man page for glam2scan

Query: glam2scan

OS: debian

Section: 1

Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar

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)
Related Man Pages
dialign-tx(1) - debian
glam2-purge(1) - debian
glam2scan(1) - debian
glam2mask(1) - debian
sigma(1) - debian
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