NAME

Bio::Tools::Run::PiseApplication::rnafold

SYNOPSIS

#

DESCRIPTION

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)

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

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.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• 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.