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

NAME
Bio::Tools::Run::PiseApplication::toppred

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::toppred

      Bioperl class for:

        TopPred Topology prediction of membrane proteins (Heijne, Wallin, Claros, Deveaud, Schuerer )

        References:

                von Heijne, G. (1992) Membrane Protein Structure Prediction: Hydrophobicity Analysis and the 'Positive Inside' Rule. J.Mol.Biol. 225, 487-494.

                Claros, M.G., and von Heijne, G. (1994) TopPred II: An Improved Software For Membrane Protein Structure Predictions. CABIOS 10, 685-686.

                Deveaud and Schuerer (Pasteur Institute) new implementation of the original toppred program, based on G. von Heijne algorithm.

      Parameters:

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

                toppred (String)

                query (Sequence)
                        Sequence

                graph_output (Switch)
                        Produce hydrophobicity graph image (-g)

                topo_output (Switch)
                        Produce image of each topology (-t)

                scale (Excl)
                        Hydrophobicity scale (-H)

                organism (Switch)
                        Organism: eukaryot (default is prokaryot) (-e)

                certain (Float)
                        Upper cutoff (-c)

                putative (Float)
                        Lower cutoff (-p)

                core (Integer)
                        Core window size:  (-n)

                triangle (Integer)
                        Wedge window size: (-q)

                loop_length (Integer)
                        Critical loop length (-s)

                Segment_distance (Integer)
                        Critical transmembrane spacer (-d)

                outformat (Excl)
                        Output format (-O)

                profile_format (Excl)
                        Hydrophobicity Profile file format

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
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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 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/toppred.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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