Module | Bio::Blast::Remote::GenomeNet |
In: |
lib/bio/appl/blast/genomenet.rb
|
The Bio::Blast::Remote::GenomeNet class contains methods for running remote BLAST searches on GenomeNet (blast.genome.jp/).
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
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 ----------+-------+---------------------------------------------------
Host | = | "blast.genome.jp".freeze |
Creates a remote BLAST factory using GenomeNet. Returns Bio::Blast object.
Note for future improvement: In the future, it might return Bio::Blast::Remote::GenomeNet or other object.
# File lib/bio/appl/blast/genomenet.rb, line 84 84: def self.new(program, db, options = []) 85: Bio::Blast.new(program, db, options, 'genomenet') 86: end