Bio::Tools::Run::PiseApplication::xpound.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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/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 (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.