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
  http://bioperl.org/wiki/Mailing_lists  - 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 the web:

  http://bugzilla.open-bio.org/

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.