NAME

Bio::Tools::Run::PiseApplication::rnaheat

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::rnaheat

      Bioperl class for:

        VIENNARNA       RNAheat - calculate specific heat of RNAs (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

                J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 11051119 D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London



      Parameters: 

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


                rnaheat (String)

                seq (Sequence)
                        RNA Sequences File

                temp_min (Integer)
                        Lowest temperature, default is 0C (-Tmin)

                temp_max (Integer)
                        Highest temperature, default is 100C (-Tmax)

                stepsize (Integer)
                        Calculate partition function every stepsize degrees C. Default is 1C (-h)

                ipoints (Integer)
                        Produces a smoother curve by increasing ipoints (-m)

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

                dangling (Excl)
                        How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)

                noGU (Switch)
                        Do not allow GU pairs (-noGU)

                noCloseGU (Switch)
                        Do not allow GU pairs at the end of helices (-noCloseGU)

                nsp (String)
                        Non standard pairs (comma seperated list) (-nsp)

                parameter (InFile)
                        Parameter file (-P)

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

                readseq (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/rnaheat.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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