Man Linux: Main Page and Category List


       glam2 - 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


       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

           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

           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).


       glam2format(1), glam2mask(1), glam2-purge(1), glam2scan(1)

       The full Hypertext documentation of GLAM2 is available online at or on this computer in


       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.