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Blast for Apple G4 and Genentech 5 times faster than on a Pentium

marzo 18, 2020

Blast for Apple G4 and Genentech 5 times faster than on a Pentium logomacitynet1200wide 1

Two top Genentech executives were sitting next to us at Steve Jobs' Keynote in San Francisco on January 7th and you should have been there to see the light in their eyes at the announcement by the Apple CEO that the first 1,000 iMac G4s had been booked by a company that sees its chairman sitting on the board of Cupertino.It was not simple satisfaction for having equipped with a machine with an unusual design and ergonomics but the awareness of having a primary research tool available.

Thanks to William Van Etten, an independent bioinformatics consultant who collaborated with both Apple and Genentech on the project, the original BLAST algorithm was brought to Mac OS X last spring and then further refined during the summer.

To give an example: the search for homology between a mouse chromosome 16 and a human one 21 using the standard NCBI size of 11 nucleotides takes 45 minutes with the version optimized for G4 while with the unmodified version it would have taken 4 hours. Blast can run on any Apple computer while the A / G Blast version can only work with G4 processors.

The improvements are available as patches for the standard NCBI version already ready for Mac OS X and can be downloaded directly from this page:

Today, Apple's official statement that reports the test performed on a 1 + 1 MHz Mac G4 Biprocessor: it is 5 times faster in performing the same calculation than a 2 GigaHertz Pentium IV

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