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glam2scan(1) [debian man page]

GLAM2SCAN(1)							   glam2 Manual 						      GLAM2SCAN(1)

NAME
glam2scan - finds a GLAM2 motif in a database SYNOPSIS
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. DESCRIPTION
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. OPTIONS (DEFAULT SETTINGS) -h Show all options and their default settings. -o Output file (stdout). -n Number of alignments to report (25). -2 Examine both strands - forward and reverse complement. -D Deletion pseudocount (0.1). -E No-deletion pseudocount (2.0). -I Insertion pseudocount (0.02). -J No-insertion pseudocount (1.0). -d Dirichlet mixture file. SEE ALSO
glam2format(1), glam2mask(1), glam2-purge(1), glam2(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 GLAM2SCAN(1)

Check Out this Related 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)
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