module Bio::Blast::Remote
Bio::Blast::Remote is a namespace for Remote Blast factory.
Constants
- Genomenet
-
Description¶ ↑
The
Bio::Blast::Remote::GenomeNetclass contains methods for running remote BLAST searches onGenomeNet(blast.genome.jp/).Usage¶ ↑
require 'bio' # To run an actual BLAST analysis: # 1. create a BLAST factory blast_factory = Bio::Blast.remote('blastp', 'nr-aa', '-e 0.0001', 'genomenet') #or: blast_factory = Bio::Blast::Remote.genomenet('blastp', 'nr-aa', '-e 0.0001') # 2. run the actual BLAST by querying the factory report = blast_factory.query(sequence_text) # Then, to parse the report, see Bio::Blast::Report
Available databases for
Bio::Blast::Remote::GenomeNet¶ ↑Up-to-date available databases can be obtained by using Bio::Blast::Remote::GenomeNet.databases(program). Short descriptions of databases
----------+-------+--------------------------------------------------- program | query | db (supported in GenomeNet) ----------+-------+--------------------------------------------------- blastp | AA | nr-aa, genes, vgenes.pep, swissprot, swissprot-upd, ----------+-------+ pir, prf, pdbstr blastx | NA | ----------+-------+--------------------------------------------------- blastn | NA | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss, ----------+-------+ htgs, dbsts, embl-nonst, embnonst-upd, epd, tblastn | AA | genes-nt, genome, vgenes.nuc ----------+-------+---------------------------------------------------
BLAST options¶ ↑
Options are basically the same as those of the blastall command in
NCBIBLAST. See www.genome.jp/tools-bin/show_man?blast2See also¶ ↑
References¶ ↑
Public Class Methods
Source
# File lib/bio/appl/blast/remote.rb 21 def self.genomenet(program, db, options = []) 22 GenomeNet.new(program, db, options) 23 #Bio::Blast.new(program, db, options, 'genomenet') 24 end
creates a remote BLAST factory using GenomeNet