[BioRuby] Batch Blasting sequences against NR-NT database

[Kevin English]

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