NAME

Bio::Tools::Run::PiseApplication::rnaga

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::rnaga

      Bioperl class for:

        RNAGA   Prediction of common secondary structures of RNAs by genetic algorithm (Chen, Le, Maizel)

        References:

                Jih-H Chen, Shu-Yun Le and Jacob Maize. Prediction of Common Secondary Structures of RNAs: A genetic Algorithm Approach, Nucleic Acids Res.,2000, Vol.28, No. 4 (991 - 999).



      Parameters: 

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


                rnaga (String)

                mv_files (String)

                seqfile (Sequence)
                        Sequence(s)
                        pipe: seqsfile

                hcrtval (Float)
                        Hcrtval: a structure is considered as a candidate of common structure during a GA iteration if the conservation score for the structure is no less than Hcrtval

                hcrtval2 (Float)
                        Hcrtval2: a structure is taken as a common secondary structure by the program if the adjusted conservation score for the structure is no less than Hcrtval2 (Normally, Hcrtval2 < Hcrtval)

                pns (Float)
                        pns: a criterion to make sure that the structure feature in a common structure is shared by majority of the sequences (pns = 0.6 means shared by at least 60% of the sequences)

                structures_nb (Integer)
                        Number of structures in a population

                iterations_nb (Integer)
                        Number of GA iterations

                beta (Float)
                        beta: a structure is considered as a candidate during a GA iteration if the free energy of the structure is no greater than (average random energy + beta * standard deviation)

                zeta (Float)
                        zeta: a structure is taken as a common structure if the free energy of the structure is no greater than (average random energy + zeta * standard deviation)

                mxdp (Integer)
                        Stem position

                mxdr (Integer)
                        Region size

                mxdL (Integer)
                        Loop size

                mxdrp (Integer)
                        Branches distance

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
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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/rnaga.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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