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Bio::Tools::Run::PiseApplication::supermatcher.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::supermatcherSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::supermatcherBioperl class for: SUPERMATCHER Finds a match of a large sequence against one or more sequences (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/supermatcher.html for available values): supermatcher (String) init (String) seqa (Sequence) seqa -- any [sequences] (-seqa) pipe: seqsfile seqb (Sequence) seqb [set of sequences] (-seqb) gapopen (Float) Gap opening penalty (-gapopen) gapextend (Float) Gap extension penalty (-gapextend) datafile (Excl) Matrix file (-datafile) width (Integer) Alignment width (-width) wordlen (Integer) word length for initial matching (-wordlen) outfile (OutFile) outfile (-outfile) pipe: readseq_ok_alig outfile_aformat (Excl) Alignment output format (-aformat) errorfile (OutFile) Error file to be written to (-errorfile) auto (String)
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/supermatcher.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 $supermatcher = Bio::Tools::Run::PiseApplication::supermatcher->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::supermatcher 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 $supermatcher = $factory->program('supermatcher'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::supermatcher.
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