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/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/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.