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Bio::Tools::Run::PiseApplication::lassap.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::lassapSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::lassapBioperl class for: LASSAP LArge Scale Sequence compArison Package (Glemet, Codani) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/lassap.html for available values): lassap (String) method (Excl) Comparison method dna_comp (Switch) nucleic/nucleic comparison query1 (Sequence) First sequence query2 (Sequence) Second sequence dr1 (String) dr2 (String) matrix (Excl) Scoring matrix gapo (Integer) Gap open penalty gape (Integer) Gap extension penalty cutoff (Integer) Cutoff Expect (Integer) Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (E) E2 (Integer) E2 (expected number of HSPs that will be found when comparing two sequences that each have the same length) S2 (Integer) S2 (cutoff score which defines HSPs) W (Integer) W (length of words identified in the query sequence) T (Integer) T (neighborhood word score threshold) X (Integer) X (word hit extension drop-off score) ktup (Integer) ktup : sensitivity and speed of the search init1 (Switch) sequences ranked by the z-score based on the init1 score noopt (Switch) no limited optimization linlen (Integer) output line length for sequence alignments (< 200) ran (Integer) How many randomizations swap (Switch) Don't test for inclusion of query1 into query2 k (Integer) How many best alignments frame_query1 (List) First sequence frames frame_query2 (List) Second sequence frames gc (Excl) Genetic Code view_alignment (Switch) View alignment (not available for all methods) scut (Integer) Score cutoff pcut (Integer) Probability cutoff max (Integer) Maximum retained flag_algo_opt (String) flag_algo_opt2 (String) gc2 (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/lassap.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 $lassap = Bio::Tools::Run::PiseApplication::lassap->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::lassap 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 $lassap = $factory->program('lassap'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::lassap.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre