Bio::Tools::Run::PiseApplication::predator # 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)

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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 the web: http://bugzilla.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) 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. This software is provided "as is" without warranty of any kind. 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.