NAME

Bio::Tools::Run::PiseApplication::dotmatcher

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::dotmatcher

      Bioperl class for:

        DOTMATCHER      Displays a thresholded dotplot of two sequences (EMBOSS)


      Parameters: 

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


                dotmatcher (String)

                init (String)

                sequencea (Sequence)
                        sequencea -- any [single sequence] (-sequencea)
                        pipe: seqfile

                sequenceb (Sequence)
                        sequenceb [single sequence] (-sequenceb)

                windowsize (Integer)
                        window size over which to test threshhold (-windowsize)

                threshold (Integer)
                        threshold (-threshold)

                matrixfile (Excl)
                        Matrix file (-matrixfile)

                stretch (Switch)
                        Stretch plot (-stretch)

                data (Switch)
                        Display as data (-data)

                graph (Excl)
                        graph [device to be displayed on] (-graph)

                xygraph (Excl)
                        xygraph (-xygraph)

                outfile (OutFile)
                        Display as data (-outfile)

                auto (String)

                psouput (String)

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/dotmatcher.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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