Provided by: glam2_1064-3_amd64
glam2scan - finds a GLAM2 motif in a database
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.
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.
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/.
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).
Martin Frith Author of GLAM2. Timothy Bailey Author of GLAM2. Charles Plessy <email@example.com> Formatted this manpage in DocBook XML for the Debian distribution.
The source code and the documentation of GLAM2 are released in the public domain.