NAME

Bio::Tools::Run::PiseApplication::dan

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::dan

      Bioperl class for:

        DAN     Calculates DNA RNA/DNA melting temperature (EMBOSS)


      Parameters: 

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


                dan (String)

                init (String)

                sequence (Sequence)
                        sequence -- DNA [sequences] (-sequence)
                        pipe: seqsfile

                windowsize (Integer)
                        Enter window size (-windowsize)

                shiftincrement (Integer)
                        Enter Shift Increment (-shiftincrement)

                dnaconc (Float)
                        Enter DNA concentration (nM) (-dnaconc)

                saltconc (Float)
                        Enter salt concentration (mM) (-saltconc)

                rna (Switch)
                        Use RNA data values (-rna)

                product (Switch)
                        Prompt for product values (-product)

                formamide (Float)
                        Enter percentage of formamide (-formamide)

                mismatch (Float)
                        Enter percent mismatch (-mismatch)

                prodlen (Integer)
                        Enter the product length (-prodlen)

                thermo (Switch)
                        Thermodynamic calculations (-thermo)

                temperature (Float)
                        Enter temperature (-temperature)

                plot (Switch)
                        Produce a plot (-plot)

                mintemp (Float)
                        Enter minimum temperature (-mintemp)

                graph (Excl)
                        graph (-graph)

                outfile (OutFile)
                        Output data file (-outfile)

                auto (String)

                psouput (String)

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/MailList.shtml  - 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 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/dan.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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