TUCSON, Ariz., Jan. 29 - Apple Computer and Genentech have partnered to develop an accelerated version of the Blast sequence alignment algorithm on Apple's G4 processor, Apple said Tuesday.
William Van Etten, an independent bioinformatics consultant who worked with Apple and Genentech on the project, announced the new capabilities during his talk on the use of Mac OS X as a bioinformatics development platform at the O'Reilly Bioinformatics Technology conference.
The project began when Van Etten ported the original NCBI Blast algorithm to OS X in the spring. Genentech and Apple's Advanced Computing Group began developing a set of Blast enhancements in mid-summer. The enhancements, which must be patched into the OS X version that is now part of NCBI's standard distribution, are freely available as of Tuesday at http://developer.apple.com/hardware/ve/acgresearch.html.
A homology search of mouse chromosome 16 against human chromosome 21 using the default NCBI word size of 11 nucleotides required 45 minutes with the enhanced version, called A/G Blast. A similar search using an unmodified version of the algorithm would take over four hours, Van Etten said.