NAME

Bio::Tools::Run::PiseApplication::mfold

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::mfold

      Bioperl class for:

        MFOLD   Prediction of RNA secondary structure (M. Zuker)

        References:

                M. Zuker, D.H. Mathews and D.H. Turner Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide in RNA Biochemistry and Biotechnology, J. Barciszewski and B.F.C. Clark, eds., NATO ASI Series, Kluwer Academic Publishers, (1999) 



      Parameters: 

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


                mfold (String)

                SEQ (Sequence)
                        Sequence File (SEQ)

                LC (Excl)
                        Sequence type (default = linear) (LC)

                NA (Excl)
                        RNA (default) or DNA (NA)

                T (Integer)
                        Temperature (T)

                P (Integer)
                        Percent (P)

                NA_CONC (Float)
                        Na+ molar concentration (NA_CONC)

                MG_CONC (Float)
                        Mg++ molar concentration (MG_CONC)

                W (Integer)
                        Window parameter (default - set by sequence length) (W)

                MAXBP (Integer)
                        MAXBP: Max base pair distance (default - no limit)

                MAX (Integer)
                        MAX: Maximum number of foldings to be computed

                ANN (Excl)
                        Structure annotation type (default=none) (ANN)

                MODE (Excl)
                        Structure display mode (default=auto) (MODE)

                ROT_ANG (Integer)
                        Structure rotation angle (ROT_ANG)

                START (Integer)
                        5' base number (START)

                STOP (Integer)
                        3' base number (default = end) (STOP)

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/mfold.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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