module Bio::Blast::Remote
Bio::Blast::Remote is a namespace for Remote Blast factory.
Constants
- Ddbj
Remote BLAST factory using DDBJ Web API for Biology (xml.nig.ac.jp/).
- Genomenet
Description¶ ↑
The Bio::Blast::Remote::GenomeNet class contains methods for running remote BLAST searches on GenomeNet (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 NCBI BLAST. See www.genome.jp/tools-bin/show_man?blast2
See also¶ ↑
References¶ ↑
Public Class Methods
ddbj(program, db, options = [])
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creates a remote BLAST factory using DDBJ Web service
# File lib/bio/appl/blast/remote.rb, line 30 def self.ddbj(program, db, options = []) DDBJ.new(program, db, options) #Bio::Blast.new(program, db, options, 'ddbj') end
genomenet(program, db, options = [])
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creates a remote BLAST factory using GenomeNet
# File lib/bio/appl/blast/remote.rb, line 24 def self.genomenet(program, db, options = []) GenomeNet.new(program, db, options) #Bio::Blast.new(program, db, options, 'genomenet') end