Bio::Tools::Run::PiseApplication::rnaga # Bio::Tools::Run::PiseApplication::rnaga Bioperl class for: RNAGA Prediction of common secondary structures of RNAs by genetic algorithm (Chen, Le, Maizel) References: Jih-H Chen, Shu-Yun Le and Jacob Maize. Prediction of Common Secondary Structures of RNAs: A genetic Algorithm Approach, Nucleic Acids Res.,2000, Vol.28, No. 4 (991 - 999). Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/rnaga.html for available values): rnaga (String) mv_files (String) seqfile (Sequence) Sequence(s) pipe: seqsfile hcrtval (Float) Hcrtval: a structure is considered as a candidate of common structure during a GA iteration if the conservation score for the structure is no less than Hcrtval hcrtval2 (Float) Hcrtval2: a structure is taken as a common secondary structure by the program if the adjusted conservation score for the structure is no less than Hcrtval2 (Normally, Hcrtval2 < Hcrtval) pns (Float) pns: a criterion to make sure that the structure feature in a common structure is shared by majority of the sequences (pns = 0.6 means shared by at least 60% of the sequences) structures_nb (Integer) Number of structures in a population iterations_nb (Integer) Number of GA iterations beta (Float) beta: a structure is considered as a candidate during a GA iteration if the free energy of the structure is no greater than (average random energy + beta * standard deviation) zeta (Float) zeta: a structure is taken as a common structure if the free energy of the structure is no greater than (average random energy + zeta * standard deviation) mxdp (Integer) Stem position mxdr (Integer) Region size mxdL (Integer) Loop size mxdrp (Integer) Branches distance

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

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