Module Bio::Blast::Remote::GenomeNet
In: lib/bio/appl/blast/genomenet.rb

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
 ----------+-------+---------------------------------------------------

See also

References

Methods

new  

Classes and Modules

Module Bio::Blast::Remote::GenomeNet::Information

Constants

Host = "blast.genome.jp".freeze

Public Class methods

new(program, db, options = [])

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.

[Source]

    # 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

[Validate]