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

Extended by:

Information

Defined in:

lib/bio/appl/blast/genomenet.rb

Overview

Description

The Bio::Blast::Remote::GenomeNet class contains methods for running remote BLAST searches on GenomeNet (http://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

• Bio::Blast
• Bio::Blast::Report
• Bio::Blast::Report::Hit
• Bio::Blast::Report::Hsp

References

• http://www.ncbi.nlm.nih.gov/blast/
• http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html
• http://blast.genome.jp/ideas/ideas.html#blast

Defined Under Namespace

Modules: Information

Constant Summary

Host =

"blast.genome.jp".freeze

Class Method Summary

• .new(program, db, options = []) ⇒ Object

  Creates a remote BLAST factory using GenomeNet.

Methods included from Information

#database_description, #databases, #nucleotide_databases, #protein_databases, #reset

Class Method Details

.new(program, db, options = []) ⇒ Object

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

def self.new(program, db, options = [])
  Bio::Blast.new(program, db, options, 'genomenet')
end