Bio::Tools::Run::PiseApplication::xpound # 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)

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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.bioperl.org/ 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. This software is provided "as is" without warranty of any kind. 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.