Bio::Tools::Run::PiseApplication::rnaga.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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
   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 (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.