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Better bioinformatics in 60 minutes


What do you get when you mix a Cray SV-1, DNA repeats, and Lesley Stahl? (No, we’re not talking about the sequel to A.I.) If you’re the NCI, you get a whole lot more productivity with technology you already own.

According to Steve Conway, head of bioinformatics at Cray, programmer Bill Long was watching the TV show “60 Minutes” one night — it happened to be about computational biology — when it hit him: The pattern-matching technology developed for classified government work was exactly what bioinformaticists needed. And conveniently, it was included on the NCI’s supercomputers. “Like most people who buy the Cray supercomputers, they didn’t even know it was there,” Conway says.

Cray and NCI met up to discuss possibilities. They spent all of this year testing and retesting the algorithms with the alternate technology. “We didn’t want to look like fools,” Conway says. But now that it’s validated, they’re practically dancing in the street.

Stan Burt, director of the Advanced Biomedical Computing Center at NCI, says this has given his computers “blinding speed.” On an average chromosome, he and his colleagues can search for repeats in five seconds. “We can do the entire human genome in less than 10 minutes,” he says.

Conway says at a minimum, the NCI’s speedup has been 40-fold, while boosts of up to 2000 times faster have been documented.

For NCI, this means scientists can generate an almost real-time database of repeats and SNPs with each update of the public genome information. Burt says the major goals are finding short and long repeats, doing BAC clone assembly, and at some point extending the procedures to proteins.

For Cray, this has opened up doors to a new potential market. Conway says it won’t affect most people. “The workaday world of the bioinformatics industry is probably going to keep using what they were using.” But that hasn’t kept everyone away. “There’s a fair number of new customers banging on our door,” he says.

— Meredith Salisbury


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