Bio::Tools::Run::PiseApplication::toppred # 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

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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/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.