glam2scan(1) 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.


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 protected]>

Formatted this manpage in DocBook XML for the Debian distribution.


The source code and the documentation of GLAM2 are released in the public domain.