Bio::Tools::Run::PiseApplication::gibbs_scan(3)

NAME
Bio::Tools::Run::PiseApplication::gibbs_scan

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::gibbs_scan

      Bioperl class for:

        GIBBS   scan a database with a sampled motif (Neuwald, Lawrence)

      Parameters:

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/gibbs_scan.html
         for available values):

                gibbs_scan (String)

                motif_file (InFile)
                        Motif scan file (file.sn)
                        pipe: gibbs_motif

                db (Excl)
                        Database

                e_value (Float)
                        Maximum E-value detected (-e)

                p_value (Float)
                        Minimum -log10(P-value) required for each motif (-E)

                repeats (Switch)
                        Scan for repeats (-r)

                max_repeats (Integer)
                        Maximum number of repeats per sequence (-M)

                min_repeats (Integer)
                        Minimum number of repeats per sequence (-m)

                order (Switch)
                        Require motifs to be in correct order (-o)

                product (Switch)
                        Use product multinomial model instead of Gribskov method (-P)

                pseudo_count (Integer)
                        Pseudo counts for product multinomial model (-p)

                shuffle (Switch)
                        Shuffle input sequences (-S)

                seed (Integer)
                        Seed for random number generator (-s)

                mask (Excl)
                        Mask out sequence regions...

                heap (Integer)
                        Size of heap for saving sequences (-h)

                seqfile (Switch)
                        Create sequence file for output (-c)

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/MailList.shtml  - 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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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_scan.html

•   Bio::Tools::Run::PiseApplication

•   Bio::Tools::Run::AnalysisFactory::Pise

•   Bio::Tools::Run::PiseJob

  new
 Title   : new()
 Usage   : my $gibbs_scan = Bio::Tools::Run::PiseApplication::gibbs_scan->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::gibbs_scan 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_scan = $factory->program('gibbs_scan');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::gibbs_scan.