Bio::Tools::Run::PiseApplication::gibbs # Bio::Tools::Run::PiseApplication::gibbs Bioperl class for: GIBBS motif sampling (Neuwald & Lawrence) References: Neuwald, Liu, and Lawrence (1995). Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Science 4, 1618-1632. (for Gibbs site sampling, Gibbs motif sampling, purge, and scan programs) Lawrence, Altschul, Boguski, Liu, Neuwald and Wootton (1993) Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment, Science 262:208-214. (for Gibbs site sampling program) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/gibbs.html for available values): gibbs (String) sequence (Sequence) Sequences file lengths (String) Lengths of elements for each type (eg: e1,e2) expected (String) Expected number of elements for each type (eg: l1,l2) (motif sampler) purge (Switch) Run purge to remove closely related sequences scan (Switch) Create a scan output file (file.sn) (-f) sites_cycles (Integer) Maximum number of cycles in each run (-m) element_order (Switch) Use element order in probabilities (-o) sites_pseudo_counts (Float) Pseudo counts for ordering model (-q) readings (Integer) Number of near-optimum readings taken (-R) wilcoxon (Switch) Output wilcoxon rank test information (-w) fractional_weight (Float) Fractional weight (0 to 1.0) on priors (-W) cycles (Integer) Number of cycles between shifts (sites sampler) or maximum number of cycles per run (motif sampler) (-c) cutoff (Float) Prob. cutoff for near optimum sampling (-C) fragmentation (Switch) Use fragmentation (-d) convergence (Integer) Rapid convergence limit (higher = longer to converge) (-L) nucleic (Switch) Use nucleic acid alphabet (-n) pseudo_counts (Float) Number of pseudo counts for product multinomial model (-p) shuffle (Switch) Randomly shuffle input sequences (-r) seed (Integer) Seed for random number generator (-s) sampling_runs (Integer) Maximum number of sampling runs (-t) low_complexity (Switch) Remove protein low complexity regions (-x) score (Integer) Score threshold method (Excl) Heuristic method keep (Switch) Keep first sequence in the set (-q) mask (Switch) Use xnu to mask low complexity regions (-x) purge_sep (String) scan_file (OutFile) pipe: gibbs_motif

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. This software is provided "as is" without warranty of any kind. http://bioweb.pasteur.fr/seqanal/interfaces/gibbs.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

new
Title : new() Usage : my $gibbs = Bio::Tools::Run::PiseApplication::gibbs->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::gibbs object. This method should not be used directly, but rather by a Bio::Tools::Run::AnalysisFactory::Pise instance. my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(); my $gibbs = $factory->program('gibbs'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::gibbs.