[Bioperl-l] Fwd: question about Bio::Tools::Run::StandAloneBlast

Robert Bradbury robert.bradbury at gmail.com
Wed Apr 14 11:43:08 EDT 2010

On Wed, Apr 14, 2010 at 9:16 AM, Chris Fields <cjfields at illinois.edu> wrote:

> I'm assuming that we will slowly be deprecating use of those modules as
> users migrate over to BLAST+.  I'm not sure, but I don't think NCBI will
> support legacy BLAST that much longer.
By "legacy BLAST" do you refer to blast submission requests from the

I ask because I use BLAST @ NCBI a fair amount and have scripts that use it.
 [Though I would be very happy for a "Blast Gateway" [Google SoC
opportunity???] that would run queries against NCBI, JGI, Ensembl & perhaps
the various Yeast/Insect/Nematode databases].  I state this because of the
genome scale efforts that I'm aware of Broad seems to be feeding the data to
Ensembl first while a lot of the data from JGI seems to take a long time to
make it to NCBI.]

I do realize that there is an some kind of an exponential growth problem
with the number of genomes sequenced and blast scans against the entire set
of genomes but I would hope that computing capacity is scaling with this.
 After all the number of species is finite.

But it would that if "free" resources for running blast scans are limited
that interfaces are going to have to move in the direction of a combined
"public"+"private" ("remote"+"local") methodology.


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