Apple Releases Apple/Genentech BLAST, Significantly Accelerating Protein and DNA Searches For The Biomedical Community

Apple today announced a breakthrough implementation of BLAST software that accelerates protein and DNA searches used in biomedical research and drug discovery. Apple/Genentech BLAST is up to five times faster than the standard BLAST implementation, the popular bioinformatics tool from the National Center for Biotechnology Information (NCBI).

Apple/Genentech BLAST provides improved accuracy and speed over the standardNCBI BLAST, depending on search parameters such as the nucleotidematch-length. For certain common searches this version enables a dual 1GHzPower Mac G4 computer to deliver more than five times the performance of acomparable 2GHz Pentium 4-based system running the standard NCBI BLAST.

“Apple and Genentech have dramatically increased the performance of animportant tool that biomedical researchers use every day”, said DavidBotstein, Ph.D., professor and chair of the Stanford University GeneticsDepartment. “I'm impressed and delighted that a machine that a regular scientist can afford and run, such as the Power Mac G4, is as fast, orfaster, than the industry standard BLAST running on more expensivemachines”.

“We're pleased to have collaborated with Apple on this project and to be able to make these performance improvements more widely available to thescientific community through the NCBI and Apple's Advanced ComputationGroup”, said Richard H. Scheller, Ph.D., senior vice president of Research, Genentech. “The Apple/Genentech BLAST will allow researchers to more efficiently utilise genomic information in basic biomedical research anddrug discovery”.

Developed by Apple's Advanced Computation Group (ACG) in collaboration with Genentech, Inc. and the Stanford University Genetics Department,Apple/Genentech BLAST is a high-throughput version of BLAST which takesadvantage of algorithmic improvements, advanced memory management and theability of Apple's PowerPC G4 processor with Velocity Engine to performmultiple operations per clock cycle.

Apple is offering this advanced version of Apple/Genentech BLAST as OpenSource software and is working with NCBI to make it easy for the biomedicalcommunity to utilise the new code as part of ongoing development. The codefor Apple/Genentech BLAST, as well as analyses of its performance, areavailable for download at:

http://developer.apple.com/hardware/ve/acgresearch.html.

The PowerPC G4 processor with Velocity Engine, coupled with the Open Source,UNIX-based core of Mac OS X, provides an incredibly productive platform forcomputational science. The ability of the Velocity Engine to pre-fetch dataand perform multiple floating-point operations per clock cycle enables it toeasily analyse the massive amounts of information coming from genome,protein and DNA sequencing projects. The newly-released dual 1GHz Power MacG4, delivering an amazing 15 gigaflops, gives life scientists a powerful yeteasy-to-use turnkey solution. Running Mac OS X, which combines the power ofUNIX with the simplicity of the Mac, the Power Mac G4 enables scientists toperform custom data analysis and use standard productivity applications onthe same desktop, reducing costs and streamlining workflow.

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