NAME

Bio::Tools::Run::PiseApplication::genscan

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::genscan

      Bioperl class for:

        GENSCAN Gene Identification (C. Burge)

        References:

                Burge, C., Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94.

                Burge, C., Karlin, S. (1997) Gene structure, exon prediction, and alternative splicing.  (in preparation).

                Burge, C. (1997) Identification of genes in human genomic DNA. PhD thesis, Stanford University, Stanford, CA.

                Burset, M., Guigo, R. (1996) Evaluation of gene structure prediction programs.  Genomics 34, 353-367.



      Parameters: 

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


                genscan (String)

                seq (Sequence)
                        DNA Sequence File
                        pipe: seqfile

                parameter_file (Excl)
                        Parameter file

                verbose (Switch)
                        Verbose output (-v)

                cds (Switch)
                        Print predicted coding sequences (-cds)

                subopt (Switch)
                        Identify suboptimal exons (-subopt)

                cutoff (Integer)
                        Cutoff for suboptimal exons

                ps (Switch)
                        Create Postscript output (-ps)

                scale (Integer)
                        Scale for PostScript output (bp per line)

                psfname (OutFile)
                        Filename for PostScript output

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/genscan.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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