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BLAST off

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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 Groupwebsite.

References

  1. 1.

    O'Reilly Bioinformatics Technology Conference, [http://www.oreillynet.com/biocon2002/]

  2. 2.

    NCBI-BLAST , [http://www.ncbi.nlm.nih.gov/BLAST/]

  3. 3.

    Apple Advanced Computation Group, [http://developer.apple.com/hardware/ve/acgresearch.html]

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Thorpe, C. BLAST off. Genome Biol 3, spotlight-20020201-01 (2002) doi:10.1186/gb-spotlight-20020201-01

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Keywords

  • Nucleotide
  • Source Code
  • Human Chromosome
  • Homology Search
  • Mouse Chromosome