Bio::Tools::Run::PiseApplication::polydot # Bio::Tools::Run::PiseApplication::polydot Bioperl class for: POLYDOT Displays all-against-all dotplots of a set of sequences (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/polydot.html for available values): polydot (String) init (String) sequences (Sequence) Sequences file to be read in (-sequences) pipe: seqsfile wordsize (Integer) Word size (-wordsize) data (Switch) Display as data (-data) graph (Excl) graph [device to be displayed on] (-graph) outfile (OutFile) outfile (-outfile) gap (Integer) Gap (in residues) between dotplots (-gap) boxit (Switch) Draw a box around each dotplot (-boxit) dumpfeat (Switch) Dump all matches as feature files (-dumpfeat) format (String) format to Dump out as (-format) ext (String) Extension for feature file (-ext) auto (String) psouput (String)

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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/polydot.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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