Molecular biologists using Apple computers can receive a speed boost if they use an optimized version of BLAST and the new Mac operating system OS X on a Macintosh G4. The new version of BLAST, called A/G BLAST, was engineered by Apple's Advanced Computation Group in conjunction with Genentech and was announced on 29 January at the O'Reilly Bioinformatics Technology Conference in Tucson Arizona. A/G BLAST is optimized to take advantage of the G4 processor's Altivec or 'Velocity Engine' components to substantially increase the speed and efficiency of running BLAST queries.
A/G BLAST outperformed BLAST dramatically in a test case of a homology search of mouse chromosome 16 against human chromosome 21 using the NCBI word size of 11 nucleotides. The optimized BLAST required only 45 minutes, compared to NCBI-BLAST on the same machine, which took over four hours.
Steve Jobs, iCEO of Apple, recently announced that Genentech were the first customers for the G4 iMac, having placed a pre-order for 1000 machines. The optimized software is available for immediate download either as source code or executable, from the Apple Advanced Computation Group website.