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glam2scan - finds a GLAM2 motif in a database

GLAM2SCAN(1) glam2 Manual GLAM2SCAN(1)


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.


Show all options and their default settings.
Output file (stdout).
Number of alignments to report (25).
Examine both strands - forward and reverse complement.
Deletion pseudocount (0.1).
No-deletion pseudocount (2.0).
Insertion pseudocount (0.02).
No-insertion pseudocount (1.0).
Dirichlet mixture file.


glam2format(1), glam2mask(1), glam2-purge(1), glam2(1)
The full Hypertext documentation of GLAM2 is available online at 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 <>
Formatted this manpage in DocBook XML for the Debian distribution.
The source code and the documentation of GLAM2 are released in the public domain.
05/19/2008 GLAM2 1056