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
  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/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.