Man page - glam2scan(1)
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Manual
GLAM2SCAN
NAMESYNOPSIS
DESCRIPTION
OPTIONS (DEFAULT SETTINGS)
SEE ALSO
REFERENCE
AUTHORS
COPYRIGHT
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.