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/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_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.