Bio::Tools::Run::PiseApplication::scan_for_matches # Bio::Tools::Run::PiseApplication::scan_for_matches Bioperl class for: scan_for_matches Scan Nucleotide or Protein Sequences for Matching Patterns Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/scan_for_matches.html for available values): scan_for_matches (String) sequence (Sequence) Input sequence pattern (String) Search pattern mismatches (Integer) Number of mismatches deletions (Integer) Number of deletions insertions (Integer) Number of insertions info_user_pattern_file (Label) Please look at the documentation for using your own patterns. user_pattern_file (InFile) You may give your own patterns complementary_strand (Switch) Search complementary strand protein (Switch) Protein stop_after_n_misses (Integer) Stop after n misses

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

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