NAME

Bio::Tools::Run::PiseApplication::xpound

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::xpound

      Bioperl class for:

        Xpound  software for exon trapping (Thomas & Skolnick)

        References:

                A probabilistic model for detecting coding regions in DNA sequences.  Alun Thomas and Mark H Skolnick,  IMA Journal of Mathematics Applied in Medicine and Biology, 1994, 11, 149-160.



      Parameters: 

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


                xpound (String)

                seq (Sequence)
                        DNA sequence File

                outfile (OutFile)

                report (Switch)
                        Reports regions of bases for which the probability of coding is high (xreport)

                cut_off (Integer)
                        Cut off value for report

                min_length (Integer)
                        Minimum length value for report

                report_file (OutFile)
                        Report file

                postscript (Switch)
                        Produces a file of graphs in PostScript format (xpscript)

                orientation (Excl)
                        Orientation

                rows (Integer)
                        Rows of plots per page (-r)

                columns (Integer)
                        Columns of plots per page (-c)

                high (Integer)
                        Draw a line at this level (-hi)

                low (Integer)
                        Draw a line at this level (-hi)

                psfile (OutFile)
                        PostScript file

                result (InFile)

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/xpound.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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