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

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/blimps.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise 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.