Bio::Tools::Run::PiseApplication::predator(3)

NAME
Bio::Tools::Run::PiseApplication::predator

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::predator

      Bioperl class for:

        PREDATOR        Protein secondary structure prediction from a single sequence or a set of sequences (D. Frishman & P. Argos)

        References:

                Frishman, D. and Argos, P. (1996) Incorporation  of  long-distance interactions  into  a  secondary structure prediction algorithm. Protein Engineering,  9, 133-142.

                Frishman,  D. and Argos,  P.  (1997)  75%  accuracy  in  protein secondary structure prediction.  Proteins,  27, 329-335.

                Frishman,D and Argos,P. (1995) Knowledge-based secondary structure assignment. Proteins:  structure,  function  and genetics, 23, 566-579.

                Kabsch,W. and Sander,C. (1983)  Dictionary  of  protein  secondary structure: pattern    recognition   of hydrogen-bonded and geometrical features. Biopolymers, 22: 2577-2637.

      Parameters:

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

                predator (String)

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

                single (Switch)
                        Perform  single  sequence  prediction. Ignore  other sequences in the set for computing the prediction (-s)

                dont_copy (Switch)
                        Do not copy assignment directly from the PDB database (-u)

                dssp (Switch)
                        Use DSSP target assignment (-d)

                percentid (Float)
                        Find a subset of sequences with no more than this identity between any pair of sequences (-n)

                all (Switch)
                        Make prediction for All sequences in the input file (-a)

                seqid (String)
                        Make prediction for this sequence (give its id) (-i)

                stride_file (InFile)
                        STRIDE file (-x)
                        pipe: stride_outfile

                dssp_file (InFile)
                        DSSP file (-y)
                        pipe: dssp_outfile

                pdb_chain (String)
                        PDB Chain (-z)

                long (Switch)
                        Long output form (-l)

                other_info (Switch)
                        Output  other  additional information if available (-h)

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/predator.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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