module Bio::Blast::Remote

Bio::Blast::Remote is a namespace for Remote Blast factory.

Constants

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

genomenet(program, db, options = []) click to toggle source

creates a remote BLAST factory using GenomeNet

# File lib/bio/appl/blast/remote.rb, line 21
def self.genomenet(program, db, options = [])
  GenomeNet.new(program, db, options)
  #Bio::Blast.new(program, db, options, 'genomenet')
end