> Is there or is there not a parallel version of blast available > somewhere? (addressing a different part of the question than Chris D.) I'm not aware of an MPI version of BLAST, nor would I use one if it was available. My problem is throughput, not response time on BLAST jobs. In this situation, anything less than a parallel effficiency of one is wasting resources. NCBI's BLAST has the "-a <NUM_CPUS>" option, which enables threading. If your operating system is intelligent about SMP and you have more than one CPU on the board, you can use it to run in parallel. I haven't studied it with any rigor, but thumbnail tests indicate that the parallel efficiency is fairly high for NUM_CPU <= 8. This is great for decreasing wait time for web users, but it doesn't address my interests at all. Not to beat it into the ground, but: It's throughput that we need. That's why we're all so fond of queuing systems and processing farms, rather than high performance parallel machines. -Chris