Provided by: glam2_1064-3_amd64
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 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.
OPTIONS (DEFAULT SETTINGS)
-h Show all options and their default settings. -o Output file (stdout). -r Number of alignment runs (10). -n End each run after this many iterations without improvement (10000). -2 Examine both strands - forward and reverse complement. -z Minimum number of sequences in the alignment (2). -a Minimum number of aligned columns (2). -b Maximum number of aligned columns (50). -w Initial number of aligned columns (20). -d Dirichlet mixture file. -D Deletion pseudocount (0.1). -E No-deletion pseudocount (2.0). -I Insertion pseudocount (0.02). -J No-insertion pseudocount (1.0). -q Weight for generic versus sequence-set-specific residue abundances (1e+99). -t Initial temperature (1.2). -c Cooling factor per n iterations (1.44). -u Temperature lower bound (0.1). -p Print progress information at each iteration. -m Column-sampling moves per site-sampling move (1.0). -x Site sampling algorithm: 0=FAST 1=SLOW 2=FFT (0). -s 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 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 <email@example.com> Formatted this manpage in DocBook XML for the Debian distribution.
The source code and the documentation of GLAM2 are released in the public domain.