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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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.