NAME

Bio::Tools::Run::PiseApplication::grailclnt

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::grailclnt

      Bioperl class for:

	GRAILCLNT	Grail client (Xu, Einstein, Mural, Shah, Uberbacher)

	References:

		Xu, Y., Einstein, J. R., Mural, R.J., Shah, M. and Uberbacher, E.C., (1994) An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequences, Published Presentation: The Second International Conference on Intelligent Systems for Molecular Biology, Stanford University, San Francisco, CA, August 14-17, 1994.



      Parameters: 

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


		grailclnt (String)

		seq (Sequence)
			Sequence

		feature (Excl)
			Which feature?

		organism (Excl)
			Organism

		header (Switch)
			Header

		translation (Switch)
			Translation

		strandscores (Switch)
			Strandscores (grail1)

		shadowexons (Switch)
			Shadowexons (grail 1.a or grail2)

		clusters (Switch)
			Clusters (grail 2)

		cluster_file (InFile)
			grail2exons results file
			pipe: grail_cluster

		modelexon_translation (Switch)
			Gene model exons translation

		genemodel_translation (Switch)
			Entire gene models translation

		auto_strand (Switch)
			AUTO STRAND

		start_strand (Integer)
			AUTO STRAND start

		end_strand (Integer)
			AUTO STRAND end

		forward_strand (Switch)
			FORWARD_STRAND

		reverse_strand (Switch)
			REVERSE_STRAND

		grail2_file (InFile)
			grail2exons results file
			pipe: grail_cluster

		fserr_strand (Excl)
			Strand

		rpttv_organism (String)

		start_seq (String)

		end_seq (String)

		end_request (String)

		outfile (OutFile)
			Result file
			pipe: grail_cluster

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/grailclnt.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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