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Bio::Tools::Run::PiseApplication::blimps.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::blimpsSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::blimpsBioperl class for: BLIMPS BLocks IMProved Searcher (Wallace, Henikoff) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/blimps.html for available values): blimps (String) action (Excl) Action blocks_db (Excl) Blocks database sequence_file (Sequence) Sequence file filename to score against blocks database sequence_db (Excl) Sequences database block_file (InFile) Block file filename matrix_file (InFile) A precomputed site specific scoring matrix file conversion (Excl) Conversion method for converting a block to a matrix genetic_code (Excl) The Genetic code to use strand (Switch) both strands to be searched outfile (OutFile) Output file filename error (Excl) Error level to report at export_matrix (OutFile) Export matrix (matricies) to this filename histogram (Switch) Print the histogram values in the output file scores_number (Integer) The number of scores to report. repeats (Switch) Repeats are allowed in the scoring list error_file (OutFile)
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/blimps.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 $blimps = Bio::Tools::Run::PiseApplication::blimps->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::blimps 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 $blimps = $factory->program('blimps'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::blimps.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre