glam2(1) Gapped Local Alignment of Motifs


glam2 [options] alphabet my_seqs.fa

An alphabet other than p or n is interpreted as the name of an alphabet file.


GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs.



Show all options and their default settings.


Output file (stdout).


Number of alignment runs (10).


End each run after this many iterations without improvement (10000).


Examine both strands - forward and reverse complement.


Minimum number of sequences in the alignment (2).


Minimum number of aligned columns (2).


Maximum number of aligned columns (50).


Initial number of aligned columns (20).


Dirichlet mixture file.


Deletion pseudocount (0.1).


No-deletion pseudocount (2.0).


Insertion pseudocount (0.02).


No-insertion pseudocount (1.0).


Weight for generic versus sequence-set-specific residue abundances (1e+99).


Initial temperature (1.2).


Cooling factor per n iterations (1.44).


Temperature lower bound (0.1).


Print progress information at each iteration.


Column-sampling moves per site-sampling move (1.0).


Site sampling algorithm: 0=FAST 1=SLOW 2=FFT (0).


Seed for pseudo-random numbers (1).


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.