>[I just finished composing this as Joe's post showed up] >Under most modern operating systems, BLAST databases automatically >get cached in memory by the OS as they are searched. The operating >system typically uses all available memory (unused by currently >active applications) to cache frequently used data from files on >disk. <snip> > >To the best of my knowledge, NCBI's blastall code uses memory-mapped >I/O whenever possible. <snip> > >A quick hack to ensure the DB stays in memory would be creating a >RAMdisk and copy the DB onto it. I think OS X supports RAMdisks.(?) I've been following this thread with interest. I can contribute this - OS X doesn't have an inbuilt ramdisk option like Os 9 had, but there are 2 programs I know of (but have not used) that you can make a ramdisk with: Disk Velox <http://www.versiontracker.com/dyn/moreinfo/macosx/24364> and Ram Disk Creator <http://www.donelleschi.com/ramdiskcreator/> - Al