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 (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

  • Bio::Blast

  • Bio::Blast::Report

  • Bio::Blast::Report::Hit

  • Bio::Blast::Report::Hsp

References

Defined Under Namespace

Modules: Information

Constant Summary

Host =
"www.genome.jp".freeze

Class Method Summary collapse

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.



87
88
89
# File 'lib/bio/appl/blast/genomenet.rb', line 87

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