Tim Cutts wrote: > > On 2 Mar 2005, at 5:59 am, James Cuff wrote: > >> mpiblast works. Really very well for certain problems. There I said >> it. >> >> Guy and Tim will probably never forgive me... I think I may have >> been the >> original 'embarrassingly parallel is the only way, nothing else will >> ever >> give the throughput, yada, yada' advocate... > > > Aargh - he's gone over to the Dark Side!!! > Haha! You guys crack me up :-) You will be assimilated. Resistance is futile. > Seriously, I agree with you. MPIBlast gets you fast turnaround for > single very large searches. I still think for the things Sanger are > doing we do better with the embarrassingly parallel model, but I > wouldn't claim that it's always the right solution (at least not any > more, he said, covering his tracks in case he's ever said exactly that > somewhere in the past) For whatever it's worth, my opinion is that there are far better -- faster *and* more sensitive -- local alignment algorithms than BLAST and it's a shame they haven't come into wide use. If (when) NCBI takes one of those better algorithms and calls it BLAST I bet it will get used. People know NCBI BLAST, people trust NCBI BLAST. As long as that remains true there will be a place for parallel NCBI BLAST, and with huge databases even database segmentation will have a place. What I really look forward to is for somebody to come up with a clever compression and searchable indexing scheme that accounts for the huge amount of redundancy in big databases like nt. Then we won't need mpiBLAST anymore. -Aaron