[BioRuby] Batch Blasting sequences against NR-NT database

[Kevin English]

This will runs a batch job. I have ruby on rails web interface but all
my blasting is handled using the DelayedJob plugin.

What do you mean by "in a pipe line"?


Kevin

On Wed, Oct 21, 2009 at 10:40 AM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> 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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>