Bio::Tools::Run::PiseApplication::siggen # Bio::Tools::Run::PiseApplication::siggen Bioperl class for: SIGGEN Generates a sparse protein signature (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/siggen.html for available values): siggen (String) init (String) algpath (InFile) Location of alignment files for input (-algpath) algextn (String) Extension of alignment files for input (-algextn) sparsity (Integer) % sparsity of signature (-sparsity) randomise (Switch) Generate a randomised signature (-randomise) seqoption (List) Select number -- Sequence variability scoring method [select values] (-seqoption) datafile (Excl) Substitution matrix to be used (-datafile) conoption (List) Select number -- Residue contacts scoring method [select values] (-conoption) filtercon (Switch) Ignore alignment positions making less than a threshold number of contacts (-filtercon) conthresh (Integer) Threshold contact number (-conthresh) conpath (String) Location of contact files for input (-conpath) conextn (String) Extension of contact files (-conextn) cpdbpath (String) Location of coordinate files for input (embl-like format) (-cpdbpath) cpdbextn (String) Extension of coordinate files (embl-like format) (-cpdbextn) filterpsim (Switch) Ignore alignment postitions with post_similar value of 0 (-filterpsim) sigextn (String) Extension of signature files for output (-sigextn) auto (String)

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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/siggen.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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