NAME
Bio::Tools::Run::PiseApplication::dialign2
SYNOPSIS
#
DESCRIPTION
Bio::Tools::Run::PiseApplication::dialign2
Bioperl 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
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
http://bioweb.pasteur.fr/seqanal/interfaces/dialign2.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
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.