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

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
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  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/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.