Hey Gang, I'm designing a system for automatic prokaryotic genome annotation. The system will need to annotate (typically several thousand) coding regions, in part by BLASTing multiple reference databases, like COGs, UNIPROT, ncbi nr etc. Im wondering about the most efficient way to do this using my Xserve cluster and mpi-blast. Im cool with prestaging the mpi-blast-formatted databases onto the compute nodes, and my intuition tells me it would be best to blast the set of coding regions against one reference database at at time, ie blast all coding regions against COGs, then again against UNIPROT, etc. That way the reference databases can stay resident in RAM for the entire blast run against the genome coding regions. Does this sound right? Will this actually happen? Would I call the mpi-blast executable once on the entire list of coding regions, or would multiple mpi-blast calls (one per coding region) achieve the same thing (keeping the database resident in RAM)? Any advice on how to implement this system for optimal mpi-blasting would be sincerely appreciated. May the force be with you, g. -- Gary Van Domselaar, PhD Associate Director, Bioinformatics.Org gary at bioinformatics.org