Bio::Tools::Run::PiseApplication::psiblast
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Bioperl class for: BLAST2 psiblast - Position Specific Iterative Blast (Altschul, Madden, Schaeffer, Zhang, Miller, Lipman) References: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaeffer,Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/psiblast.html for available values): psiblast (String) query (Sequence) Sequence File 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) protein_db (Excl) protein db 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_y (Float) Dropoff for blast ungapped extensions in bits (-y) gapped_alig (Switch) Perform gapped alignment (-g) 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) max_passes (Integer) Maximum number of passes to use in multipass version (-j) expect_in_multipass (Float) e-value threshold for inclusion in multipass model (-h) pseudocounts (Integer) Constant in pseudocounts for multipass version (-c) trigger (Float) Number of bits to trigger gapping (-N) Descriptions (Integer) How many short descriptions? (-v) Alignments (Integer) How many alignments? (-b) view_alignments (Excl) Alignment view options (not with blastx/tblastx) (-m) htmloutput (Switch) HTML output seqalign_file (OutFile) SeqAlign file (-J option must be true) (-O) believe (Switch) Believe the query defline (-J) save_matrix (OutFile) Save PSI-Blast Matrix to file (-C) pipe: psiblast_matrix save_txt_matrix (OutFile) Save PSI-BLAST Matrix as text to file (-Q) nb_proc (Integer)
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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/psiblast.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob
Title : new() Usage : my $psiblast = Bio::Tools::Run::PiseApplication::psiblast->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::psiblast 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 $psiblast = $factory->program('psiblast'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::psiblast.
To install Bio::Factory::EMBOSS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Factory::EMBOSS
CPAN shell
perl -MCPAN -e shell install Bio::Factory::EMBOSS
For more information on module installation, please visit the detailed CPAN module installation guide.