Bio::Tools::Run::PiseApplication::rnafold # Bio::Tools::Run::PiseApplication::rnafold Bioperl class for: VIENNARNA RNAfold - calculate secondary structures of RNAs (Hofacker, Fontana, Bonhoeffer, 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 A. Walter, D Turner, J Kim, M Lyttle, P Muller, D Mathews, M Zuker Coaxial stacking of helices enhances binding of oligoribonucleotides. PNAS, 91, pp 9218-9222, 1994 M. Zuker, P. Stiegler (1981) Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information, Nucl Acid Res 9: 133-148 J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 11051119 D.H. Turner N. Sugimoto and S.M. Freier (1988) RNA structure prediction, Ann Rev Biophys Biophys Chem 17: 167-192 D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/rnafold.html for available values): rnafold (String) seq (Sequence) RNA Sequences File partition (Switch) Calculate the partition function and base pairing probability matrix (-p) pf (Switch) Calculate the pf without pairing matrix (-p0) 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 (Excl) How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d) scale (Integer) Use scale*mfe as an estimate for the free energy (-S) constraints (Switch) Calculate structures subject to constraints (-C) noLP (Switch) Avoid lonely pairs (helices of length 1) (-noLP) 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) outfile (OutFile) Result file pipe: rnafold_struct b2ct (Switch) converts the bracket notation produced by RNAfold into an .ct file, as produced by Zukers mfold 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/rnafold.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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