NAME

Bio::Tools::Run::PiseApplication::dsc

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::dsc

      Bioperl class for:

        DSC     Discrimination of protein Secondary structure Class (R. D. King, M.J.E. Sternberg)

        References:

                Identification and application of the concepts important for accurate and reliable protein secondary structure prediction by Ross D. King and Michael J.E. Sternberg (Protein Science). 



      Parameters: 

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


                dsc (String)

                seq (Sequence)
                        Protein sequence(s) File
                        pipe: readseq_ok_alig

                poorly (Switch)
                        Turn off removal of poorly Aligned sections (-a)

                isolated (Switch)
                        Stop automatic removal of Isolated predictions (-i)

                filtering (Integer)
                        Level of Filtering of predictions (-f)

                seqlen (Integer)
                        Length of sequence used to determine poor alignment (-l)

                identity (Integer)
                        Threshold peRcentage of identity used to determine poor alignment (-r)

                casp (Switch)
                        CASP output format (-c)

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/dsc.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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