On Tuesday 05 Oct 2004 19:33, Ruotti, Victor wrote: > Hi, > I agree with Chris on this. BLAST databases are flat files indexed by the > formatdb program. Does anybody know whether the latest version of > formatdb allows you to index BLAST databases directly into memory? I > don't remember whether formatdb does this or not. Can somebody comment on > other methods to put BLAST databases into memory? > I am unclear of the advantage of formatdb directly to memory - it will not persist anyway. I suspect the effect observed is from the propensity or otherwise of the OS to cache recently-read files blocks in memory. With Linux, this can often be observed just by typing "cat foo.file > /dev/null" and using the file immediately thereafter. Also with multiple CPUs (in the 8-way IBM) and presumably blast jobs running on many of them almost continuously, the cached blocks remain in the cache. Perhaps OS-X file cache purges/does not cache recently read blocks more readily. I assume you do have plenty of RAM so cached disk blocks don't get purged. Those BLASTDB files can get quite large and will be at least partly purged if memory pressure occurs. Just my $0.02 worth. Regards, David Huen