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Bio::Tools::Run::PiseApplication::cds.3pm
Langue: en
Version: 2005-10-09 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tools::Run::PiseApplication::cdsSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::cdsBioperl class for: CDS Search Coding Regions (F. Chauveau) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/cds.html for available values): cds (String) seq (Sequence) Sequence File minaa (Integer) Minimum number of amino acids in CDS frame (Excl) Frame starts (String) START codons (separated by commas) maxf (Switch) longest CDS in each frame max (Switch) longest CDS all (Switch) all CDS, including CDS inside CDS nucl (Switch) nucleotids output print_adn (Switch) Print ADN as well as Amino-acids left_adn (Integer) How many base pairs on the left (if print ADN) print_frame (Switch) print frame before search print_pos (Switch) print only position(s) xml (Switch) XML output (-x) xmldtdcopy (String) end_stop (Switch) CDS ends at STOP genetic (Excl) Genetic Code
FEEDBACK
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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:
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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/cds.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 $cds = Bio::Tools::Run::PiseApplication::cds->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::cds 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 $cds = $factory->program('cds'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::cds.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre