NAME

Bio::Tools::Run::PiseApplication::rnapdist

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::rnapdist

      Bioperl class for:

	VIENNARNA	RNApdist - calculate distances of thermodynamic RNA secondary structures ensembles (Stadler, Hofacker, Bonhoeffer)

	References:

		Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P, (1993) RNA multistructure landscapes, Euro Biophys J:22,13-24



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/rnapdist.html 
         for available values):


		rnapdist (String)

		seq (Sequence)
			RNA Sequences File

		compare (Excl)
			Which comparisons (-X)

		alignment_file (OutFile)
			Alignment file (-B)

		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)

		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)

		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/rnapdist.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

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