By Salvatore Salamone

March 7, 2002 | Apple has teamed with Genentech Inc. and Stanford University’s Genetics Department to develop a faster version of the common sequence analysis tool BLAST (Basic Local Alignment Search Tool).

Apple/Genentech’s BLAST improves the time to do a nucleotide or protein search by taking advantage of optimized search algorithms and advanced memory management techniques developed by Apple’s Advanced Computation Group. The implementation also benefits from the PowerPC G4 processor’s Velocity Engine, which handles data more efficiently.

Apple computers are a familiar sight in biomedical laboratories, but now their utility extends to serious research. “[It’s good that] a machine that regular scientists can afford and run is as fast or faster than standard BLAST running on more expensive machines,” says David Botstein, chair of Stanford’s Genetics Department.

The companies say their BLAST runs up to five times faster than standard BLAST implementations. But “it’s not just faster,” says Ernest Prabhakar, Apple’s product manager of development frameworks. “[Researchers] can do searches they would never have bothered to do before.”

For example, most BLAST searches are optimized for a search string of a certain length. Shorter strings produce too many false positives whereas longer strings can take too long to perform. With the optimized version of BLAST running on a Macintosh computer, researchers would have the flexibility to do more of these types of searches, according to Prabhakar.

Developing the enhanced version of BLAST and making it available as open source software is part of Apple’s subtle bioinformatics strategy. “For the last 10 years, life scientists have had Macs and Unix machines,” says Prabhakar. He notes that the Mac OS X operating system, combined with current hardware, essentially give researchers a combination of the two with the familiar Mac user interface.