/ 
bioperl-run-1.4
/ Bio::Tools::Run::PiseApplication::predator

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.