Bio::Tools::Run::PiseApplication::mfold # Bio::Tools::Run::PiseApplication::mfold Bioperl class for: MFOLD Prediction of RNA secondary structure (M. Zuker) References: M. Zuker, D.H. Mathews and D.H. Turner Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide in RNA Biochemistry and Biotechnology, J. Barciszewski and B.F.C. Clark, eds., NATO ASI Series, Kluwer Academic Publishers, (1999) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/mfold.html for available values): mfold (String) SEQ (Sequence) Sequence File (SEQ) LC (Excl) Sequence type (default = linear) (LC) NA (Excl) RNA (default) or DNA (NA) T (Integer) Temperature (T) P (Integer) Percent (P) NA_CONC (Float) Na+ molar concentration (NA_CONC) MG_CONC (Float) Mg++ molar concentration (MG_CONC) W (Integer) Window parameter (default - set by sequence length) (W) MAXBP (Integer) MAXBP: Max base pair distance (default - no limit) MAX (Integer) MAX: Maximum number of foldings to be computed ANN (Excl) Structure annotation type (default=none) (ANN) MODE (Excl) Structure display mode (default=auto) (MODE) ROT_ANG (Integer) Structure rotation angle (ROT_ANG) START (Integer) 5' base number (START) STOP (Integer) 3' base number (default = end) (STOP)

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

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