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.
−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 <plessy@debian.org>
Formatted this manpage in DocBook XML for the Debian distribution. |
The source code and the documentation of GLAM2 are released in the public domain.