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Bio::Tools::Run::PiseApplication::genscan.3pm
Langue: en
Version: 2005-10-09 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tools::Run::PiseApplication::genscanSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::genscanBioperl 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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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
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- http://bioweb.pasteur.fr/seqanal/interfaces/genscan.html
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- Bio::Tools::Run::PiseApplication
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- Bio::Tools::Run::AnalysisFactory::Pise
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- 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.
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