Bio::Tools::Run::PiseApplication::lassap # Bio::Tools::Run::PiseApplication::lassap Bioperl 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)

Mailing Lists
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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.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) 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. This software is provided "as is" without warranty of any kind. http://bioweb.pasteur.fr/seqanal/interfaces/lassap.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise 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.