Bio::Tools::Run::PiseApplication::rnadistance # Bio::Tools::Run::PiseApplication::rnadistance Bioperl class for: VIENNARNA RNAdistance - calculate distances of RNA secondary structures (Fontana, Hofacker, Stadler) References: Shapiro B A, (1988) An algorithm for comparing multiple RNA secondary structures, CABIOS 4, 381-393 Shapiro B A, Zhang K (1990) Comparing multiple RNA secondary structures using tree comparison, CABIOS 6, 309-318 Fontana W, Konings D A M, Stadler P F, Schuster P, (1993) Statistics of RNA secondary structures, Biopolymers 33, 1389-1404 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/rnadistance.html for available values): rnadistance (String) struct (InFile) Structures File distance (Excl) Representation for distance calculation (-D) compare (Excl) Which comparisons (-X) do_analyse (Switch) Do this analysis (with AnalyseDists program) (-Xm only)? method (Excl) Analysis methods to be used (-X) shapiro (Switch) Use the Bruce Shapiro's cost matrix for comparing coarse structures (-S) alignment_file (OutFile) Alignment file (-B)

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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/rnadistance.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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