Bio::Tools::Run::PiseApplication::genscan # Bio::Tools::Run::PiseApplication::genscan Bioperl class for: GENSCAN Gene Identification (C. Burge) References: Burge, C., Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94. Burge, C., Karlin, S. (1997) Gene structure, exon prediction, and alternative splicing. (in preparation). Burge, C. (1997) Identification of genes in human genomic DNA. PhD thesis, Stanford University, Stanford, CA. Burset, M., Guigo, R. (1996) Evaluation of gene structure prediction programs. Genomics 34, 353-367. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/genscan.html for available values): genscan (String) seq (Sequence) DNA Sequence File pipe: seqfile parameter_file (Excl) Parameter file verbose (Switch) Verbose output (-v) cds (Switch) Print predicted coding sequences (-cds) subopt (Switch) Identify suboptimal exons (-subopt) cutoff (Integer) Cutoff for suboptimal exons ps (Switch) Create Postscript output (-ps) scale (Integer) Scale for PostScript output (bp per line) psfname (OutFile) Filename for PostScript output

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

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