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Bio::Tools::Run::PiseApplication::combat.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::combatSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::combatBioperl class for: COMBAT Comparison of coding DNA (Pedersen, Lyngso,Hein) References: Christian N. S. Pedersen, Rune B. Lyngso and Jotun Hein. Comparison of coding DNA in Proceedings of the 9th Annual Symposium of Combinatorial Pattern Matching (CPM), 1998. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/combat.html for available values): combat (String) sequence1 (Sequence) First Sequence sequence2 (Sequence) Second Sequence output_aln (OutFile) alignment_file (OutFile) pipe: readseq_ok_alig protein_distance_matrix (Excl) Amino-acid distance matrix nucleotide_distance_matrix (Excl) Nucleotid distance matrix protein_gap_open (Integer) Gap open cost for protein protein_gap_ext (Integer) Gap extension cost for protein dna_gap_open (Integer) Gap open cost for dna dna_gap_ext (Integer) Gap extension cost for dna gnuplot_call (String) gnuplot_commands (String)
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.open-bio.org/
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/combat.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 $combat = Bio::Tools::Run::PiseApplication::combat->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::combat 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 $combat = $factory->program('combat'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::combat.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre