[BioRuby] RPS Blast using Bioruby...

[Sharvari Gujja]

Hi all,

This is in reference to my earlier email on how to fetch CDD output from 
NCBI.

Like I said I am also trying to do RPS Blast on CDD database using 
Bio::Blast.

This is what I am trying to do:

#!/usr/bin/env ruby
require 'bio'
program = 'blastp'
db = 'nr-aa'
fasta = File.open("input1" , "r+")
blast = Bio::Blast.remote(program,db,'-e 1e-10')
report = blast.query(fasta.read)
report.each do |hit|
puts hit.target_id
end

How can I do rps blast on cdd?

Thanks
S