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Bio::Tools::Run::PiseApplication::dialign2.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::dialign2SYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::dialign2Bioperl class for: DIALIGN DNA and protein sequence alignment based on segment-to-segment comparison (Morgenstern, Dress, Werner) References: B. Morgenstern (1999). DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211 - 218. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/dialign2.html for available values): dialign2 (String) sequence (Sequence) Sequences pipe: seqsfile protein_dna (Excl) Nucleic acid or protein alignment threshold (Float) Threshold translation (Switch) Translation of nucleotide diagonals into peptide diagonals (DNA) max_simil (Integer) Maximum number of * characters representing degree similarity fasta (Switch) Alignment in fasta format
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: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/dialign2.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 $dialign2 = Bio::Tools::Run::PiseApplication::dialign2->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::dialign2 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 $dialign2 = $factory->program('dialign2'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::dialign2.
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