NAME

Bio::Tools::Run::PiseApplication::melting

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::melting

      Bioperl class for:

        MELTING enthalpie, entropy and melting temperature (N. Le Novere)

        References:

                Nicolas Le Novere (2001), MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics 17(12), 1226-1227



      Parameters: 

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


                melting (String)

                hybridation_type (Excl)
                        Hybridisation type (-H)

                nnfile (Excl)
                        Nearest Neighbor parameters set (-A)

                sequence (String)
                        Sequence string (-S)

                complement_string (String)
                        Complementary sequence (-C)

                salt_concentratio (Float)
                        Salt concentration (0.0 < x < 10.0 M) (-N)

                nucacid_concentration (Float)
                        Nucleic acid concentration in excess (0.0 < x < 0.1 M) (-P)

                correction_factor (Float)
                        Nucleic acid correction factor (-F)

                salt_correction (Excl)
                        Salt correction (-K)

                approx (Switch)
                        Force approximative temperature computation (-x)

                dangling ends (Switch)
                        parameters for dangling ends: dnadnade.nn

                mismatches (Switch)
                        nn parameters for mismatches: dnadnamm.nn

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/melting.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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