Bio::Tools::Run::PiseApplication::bl2seq # Bio::Tools::Run::PiseApplication::bl2seq Bioperl class for: BL2SEQ Blast on 2 sequences (NCBI) (Altschul, Madden, Schaeffer, Zhang, Miller, Lipman) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/bl2seq.html for available values): bl2seq (Excl) Blast program first_sequence (Sequence) First sequence (-i) pipe: seqfile first_seq_loc (String) Location on first sequence (-I) second_sequence (Sequence) Second sequence (-j) second_seq_loc (String) Location on second sequence (-J) Expect (Float) Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (-e) filter (Switch) Filter query sequence (DUST with blastn, SEG with others) (-F) other_filters (Excl) Filtering options (-F must be true) lower_case (Switch) Use lower case filtering (-U) word_size (Integer) Wordsize (-W) (zero invokes default behavior) gapped_alig (Switch) Perform gapped alignment (-g) dropoff (Integer) X dropoff value for gapped alignment (in bits) (-X) gap_open (Integer) Cost to open a gap (-G) gap_extend (Integer) Cost to extend a gap (-E) matrix (Excl) Matrix (-M) mismatch (Integer) Penalty for a nucleotide mismatch (-q) match (Integer) Reward for a nucleotide match (-r) strand (Excl) Query strands to search against database (-S) dbsize (Integer) theor. db size (zero is real size) (-d) searchspacesize (Float) Effective length of the search space (use zero for the real size) (-Y) outformat (Excl) Output format (-D)

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/bl2seq.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

new
Title : new() Usage : my $bl2seq = Bio::Tools::Run::PiseApplication::bl2seq->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::bl2seq 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 $bl2seq = $factory->program('bl2seq'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::bl2seq.