Bio::Tools::Run::PiseApplication::rnadistance(3)

NAME
Bio::Tools::Run::PiseApplication::rnadistance

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::rnadistance

      Bioperl class for:

        VIENNARNA       RNAdistance - calculate distances of RNA secondary structures (Fontana, Hofacker, Stadler)

        References:

                Shapiro B A, (1988) An algorithm for comparing multiple RNA secondary structures, CABIOS 4, 381-393 Shapiro B A, Zhang K (1990) Comparing multiple RNA secondary structures using tree comparison, CABIOS 6, 309-318

                Fontana W, Konings D A M, Stadler P F, Schuster P, (1993) Statistics of RNA secondary structures, Biopolymers 33, 1389-1404 I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125, 167-188

      Parameters:

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

                rnadistance (String)

                struct (InFile)
                        Structures File

                distance (Excl)
                        Representation for distance calculation (-D)

                compare (Excl)
                        Which comparisons (-X)

                do_analyse (Switch)
                        Do this analysis (with AnalyseDists program) (-Xm only)?

                method (Excl)
                        Analysis methods to be used (-X)

                shapiro (Switch)
                        Use the Bruce Shapiro's cost matrix for comparing coarse structures (-S)

                alignment_file (OutFile)
                        Alignment file (-B)

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
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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 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/rnadistance.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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