glam2(1) [debian man page]
GLAM2(1) glam2 Manual GLAM2(1) NAME
glam2 - Gapped Local Alignment of Motifs SYNOPSIS
glam2 [options] alphabet my_seqs.fa An alphabet other than p or n is interpreted as the name of an alphabet file. DESCRIPTION
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). SEE ALSO
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/. REFERENCE
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). AUTHORS
Martin Frith Author of GLAM2. Timothy Bailey Author of GLAM2. Charles Plessy <plessy@debian.org> Formatted this manpage in DocBook XML for the Debian distribution. COPYRIGHT
The source code and the documentation of GLAM2 are released in the public domain. GLAM2 1056 05/19/2008 GLAM2(1)
Check Out this Related Man Page
GLAM2-PURGE(1) glam2 Manual GLAM2-PURGE(1) NAME
glam2-purge - Removes redundant sequences from a FASTA file SYNOPSIS
glam2-purge file score [options] DESCRIPTION
glam2-purge is a modified version of Andrew Neuwald's purge program that removes redundant sequences from a FASTA file. This is recommended in order to prevent highly similar sequences distorting the search for motifs. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. The output file is named <file>.<score>. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA. Purge can also be used to mask tandem repeats. It uses the XNU program for this purpose. OPTIONS
-n Sequences are DNA (default: protein). -b Use blast heuristic method (default for protein). -e Use an exhaustive method (default for DNA). -q Keep first sequence in the set. -x Use xnu to mask protein tandem repeats. SEE ALSO
glam2(1), glam2format(1), glam2mask(1), glam2scan(1), xnu(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/. REFERENCES
Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618-1632, 1995. Please cite it if you use Purge. 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). AUTHORS
Andrew Neuwald Author of purge, renamed glam2-purge in Debian. Martin Frith Modified purge to be ANSI standard C and improved the user interface. Timothy Bailey Modified purge to be ANSI standard C and improved the user interface. Charles Plessy <plessy@debian.org> Formatted this manpage in DocBook XML for the Debian distribution. COPYRIGHT
The source code and the documentation of Purge and GLAM2 are released in the public domain. GLAM2 1056 05/19/2008 GLAM2-PURGE(1)