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BLAST off

Christopher Thorpe

Author Affiliations

Genome Biology 2002, 3:spotlight-20020201-01  doi:10.1186/gb-spotlight-20020201-01

The electronic version of this article is the complete one and can be found online at:


Published:1 February 2002

© 2002 BioMed Central Ltd

Research news

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.

References

  1. [http://www.oreillynet.com/biocon2002/] webcite

    O'Reilly Bioinformatics Technology Conference

  2. [http://www.ncbi.nlm.nih.gov/BLAST/] webcite

    NCBI-BLAST

  3. [http://developer.apple.com/hardware/ve/acgresearch.html] webcite

    Apple Advanced Computation Group