Bio::Tools::Run::PiseApplication::rnasubopt(3)

NAME
Bio::Tools::Run::PiseApplication::rnasubopt

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::rnasubopt

      Bioperl class for:

        VIENNARNA       RNAsubopt - calculate suboptimal secondary structures of RNAs (Wuchty, Hofacker, Fontana)

        References:

                S. Wuchty, W. Fontana, I. L. Hofacker and P. Schuster Complete Suboptimal Folding of RNA and the Stability of Secondary Structures, Biopolymers, 49, 145-165 (1999)

      Parameters:

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

                rnasubopt (String)

                seq (Sequence)
                        RNA Sequences File

                temperature (Integer)
                        Rescale energy parameters to a temperature of temp C. (-T)

                tetraloops (Switch)
                        Do not include special stabilizing energies for certain tetraloops (-4)

                mfe (Integer)
                        Calculate suboptimal structures within this range kcal/mol of the mfe (-e)

                lodos (Switch)
                        Calculate the Lower Density of States (-lodos)

                dangling (Excl)
                        How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)

                logML (Switch)
                        Recalculate energies of structures using a logarithmic energy function for multi-loops (-logML)

                ep (Integer)
                        Only print structures with energy within this prange of the mfe (with -logML) (-ep)

                sort (Switch)
                        Sort the structures by energy (-sort)

                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)

                readseq (String)

FEEDBACK

  Mailing Lists
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  bioperl-l@bioperl.org              - General discussion
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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/

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/rnasubopt.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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