[BioRuby] Batch Blasting sequences against NR-NT database

[Pjotr Prins]

Hi Kevin,

I am doing something like that in a pipe line. Do want to provide a
web interface, or is it batch based? What is the user interface you
envision?

Pj.

On Wed, Oct 21, 2009 at 07:59:13AM -1000, Kevin English wrote:
> Hi,
>   I am developeing a program where users want to blast 1000's of
> sequences against NCBI-NR database. I'm looking for advice on the best
> way to implement this. The 2 options that I see available are:
> 1) Use Bio::Blast::Remote library in the bio-ruby API.
> 2) Download the NR database from here: ftp://ftp.ncbi.nih.gov/blast/db
> and run blast locally.
> 
> Can anyone tell me, looking at this page:
> 
> http://blast.ncbi.nlm.nih.gov/blast_overview.shtml
> 
> Is the Bio::Blast::Remote using the Blastcl3 program or BLAST URL API?
> and what are the trade offs?
> 
> My project is avaible on github although I haven't finished all the
> documentation yet.
> 
> http://github.com/kenglishhi/biococonutisland
> 
> Thanks,
> 
> Kevin
> 
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