[BioRuby] RPS Blast using Bioruby...

[Naohisa GOTO]

Hi, 

Currently, RPS-Blast is not suppoted in BioRuby.

In addition, currently, Bio::Blast in BioRuby does not support
remote BLAST on NCBI. It supports GenomeNet or stand-alone BLAST.

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 10 Apr 2008 15:34:29 -0400
Sharvari Gujja <sgujja at broad.mit.edu> wrote:

> 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
>