Bio::DDBJ::XML::Blast

Description

DDBJ XML BLAST Database Search

• xml.nig.ac.jp/doc/Blast.txt

Examples

serv = Bio::DDBJ::XML::Blast.new
program = 'blastp'
database = 'SWISS'
query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"

report = serv.searchSimple(program, database, query)
Bio::Blast::Default::Report.new(report).each_hit do |hit|
  hit.hsps.find_all {|x| x.evalue < 0.1 }.each do |hsp|
    p [hsps.evalue, hsps.identity, hsps.definition]
  end
end

program = 'tblastn'
database = 'ddbjvrl'
param = '-m 8 -e 0.001'
puts serv.searchParam(program, database, query, param)

WSDL Methods

• searchSimple(program, database, query)

Returns a blast report in the default format.

• searchParam(program, database, query, param)

Blasts with param and returns a blast report.

References

• xml.nig.ac.jp/doc/Blast.txt