NAME

Bio::Tools::Run::PiseApplication::nnssp

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::nnssp

      Bioperl class for:

        NNSSP   Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignment (Salamov & Solovyev)

        References:

                Salamov AA, Solovyev VV (1995) Prediction of protein secondary structure by combinin nearest-neighbr algorithms and multiple sequence alignment. J Mol Biol, 247 : 11-15



      Parameters: 

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


                nnssp (String)

                infile (Sequence)
                        Clustalw Alignment File
                        pipe: readseq_ok_alig

                seq (String)
                        Name of the sequence to analyze

                outfile (OutFile)
                        Output File

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/nnssp.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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