NAME

Bio::Tools::Run::PiseApplication::gibbs

SYNOPSIS

  #

DESCRIPTION

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

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

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.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• 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.