NAME

Bio::Tools::Run::PiseApplication::rnaeval

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::rnaeval

      Bioperl class for:

        VIENNARNA       RNAeval - calculate energy of RNA sequences on given secondary structure (Hofacker, Stadler)

        References:

                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/rnaeval.html 
         for available values):


                rnaeval (String)

                seqstruct (InFile)
                        Sequences/Structures File (output of RNAfold)
                        pipe: rnafold_struct

                temperature (Integer)
                        Rescale energy parameters to a temperature of temp C. (-T)

                tetraloops (Switch)
                        Do not include special stabilizing energies for certain tetraloops (-4)

                dangling (Switch)
                        Don't give stabilizing energies to single stacked bases in dangling ends (-d)

                d2 (Switch)
                        Treat dangling ends as in the partition function algorithm (-d2)

                logML (Switch)
                        Let multiloop energies depend logarithmically on the size (-logML)

                parameter (InFile)
                        Parameter file (-P)

                energy (Excl)
                        Energy parameters for the artificial ABCD... alphabet (-e)

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/rnaeval.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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