Bio::Tools::Run::PiseApplication::rnaheat # 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)

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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 the web: http://bugzilla.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) 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. This software is provided "as is" without warranty of any kind. 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.