Bio::Tools::Run::PiseApplication::rnaeval # 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)

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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/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.