Bio::Tools::Run::PiseApplication::blimps_matrix # Bio::Tools::Run::PiseApplication::blimps_matrix Bioperl class for: BLIMPS score a block or matrix against a database of sequences (Wallace & Henikoff) References: J.C. Wallace and S. Henikoff, PATMAT: a searching and extraction program for sequence, pattern and block queries and databases, CABIOS, 8:3, p. 249-254 (1992). Steven Henikoff and Jorja G. Henikoff, Automated assembly of protein blocks for database searching, Nucleic Acids Research, 19:23, p. 6565-6572. (1991) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/blimps_matrix.html for available values): blimps_matrix (String) action (String) sequence_db (Excl) Sequences database block_file (InFile) Block file conversion (Excl) Conversion method for converting a block to a matrix matrix_file (InFile) A precomputed site specific scoring matrix file (instead of block file) genetic_code (Excl) The Genetic code to use (if DNA sequence or database) strands (Integer) The number of strands to search (if DNA sequence or database) 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 (Integer) The number of scores to report. repeats (Switch) Repeats are allowed in the scoring list

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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/blimps_matrix.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

new
Title : new() Usage : my $blimps_matrix = Bio::Tools::Run::PiseApplication::blimps_matrix->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::blimps_matrix 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_matrix = $factory->program('blimps_matrix'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::blimps_matrix.