Open Access

BLAST off

  • Christopher Thorpe
Genome Biology20023:spotlight-20020201-01

DOI: 10.1186/gb-spotlight-20020201-01

Published: 1 February 2002

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. O'Reilly Bioinformatics Technology Conference, [http://www.oreillynet.com/biocon2002/]
  2. NCBI-BLAST , [http://www.ncbi.nlm.nih.gov/BLAST/]
  3. Apple Advanced Computation Group, [http://developer.apple.com/hardware/ve/acgresearch.html]

Copyright

© BioMed Central Ltd 2002

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