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 >