[Bioclusters] mpiBLAST Performance

[Lucas Carey]

Has anyone looked into why there is such a large speedup when shuffling the database? Does this hold for the query as well? Are you just randomizing the db sequence entries? 

-Lucas

On Wed, May 14, 2003 at 11:50:31AM -0400, Joe Landman wrote:
> On Wed, 2003-05-14 at 11:43, Jason D. Gans wrote:
> 
> > Also, while not a factor when blasting against the nr database, shuffling the 
> > nt database yields a substantial speed increase in blast searches (I have obtained
> > a 28% decrease in wall clock time for certain nucleotide queries).
> 
> I noted in 1999 and 2000 while working on GenomeCluster that a query
> sequence "sort" or shuffle sometimes helped.  I didn't do that on the db
> side due to the time costs of the operation.  Maybe worth a re-look.
> 
> 
> -- 
> Joseph Landman, Ph.D
> Scalable Informatics LLC,
> email: landman@scalableinformatics.com
> web  : http://scalableinformatics.com
> phone: +1 734 612 4615
>