Bio::Tools::Run::PiseApplication::phiblast # Bio::Tools::Run::PiseApplication::phiblast Bioperl class for: BLAST2 phi-blast - Pattern-Hit Initiated BLAST (Altschul, Madden, Schaeffer, Zhang, Miller, Lipman) References: R. Baeza-Yates and G. Gonnet, Communications of the ACM 35(1992), pp. 74-82. S. Wu and U. Manber, Communications of the ACM 35(1992), pp. 83-91. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/phiblast.html for available values): phiblast (Excl) Program (-p) nb_proc (Integer) query (Sequence) Sequence File (-i) pipe: seqfile start_region (Integer) Start of required region in query (-S) end_region (Integer) End of required region in query (-1 indicates end of query) (-H) pattern (String) Pattern - Prosite syntax (-k) protein_db (Excl) protein db (-d) filter (Switch) Filter query sequence with SEG (-F) Expect (Integer) Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (-e) window (Integer) Multiple hits window size (zero for single hit algorithm) (-A) extend_hit (Integer) Threshold for extending hits (-f) dropoff (Integer) X dropoff value for gapped alignment (in bits) (-X) dropoff_z (Integer) X dropoff value for final gapped alignment (in bits) (-Z) matrix (Excl) Matrix (-M) open_a_gap (Integer) Cost to open a gap (-G) extend_a_gap (Integer) Cost to extend a gap (-E) Descriptions (Integer) How many short descriptions? (-v) Alignments (Integer) How many alignments? (-b) view_alignments (Excl) Alignment view options (not with blastx/tblastx) (-m) html_output (String) Html output seqalign_file (OutFile) SeqAlign file (-J option must be true) (-O) believe (Switch) Believe the query defline (-J) txtoutput (String)

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

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