Late last year, while watching a news report that examined the challenges of annotating the human genome sequence, Bill Long had an epiphany. A programmer at Seattle-based Cray Inc., Long realized that many bioinformatics complexities are basically problems of pattern matching--a Cray specialty. So, Long phoned the National Cancer Institute's (NCI) Advanced Biomedical Computing Center (ABCC) and suggested a collaboration. He was well received. Says ABCC director Stan Burt, facility researchers "pride [themselves] on being able to translate biological problems into computational [ones]."

The key to Long's idea centered on four pieces of hardware found inside each Cray computer. Distinct from the computer's central processing unit, these pieces, when acting in concert, are extraordinarily efficient at pattern matching. This hardware and its associated instruction set were first developed for the intelligence community. Most other users of these computers neither know nor care that this hardware exists, says Steve Conway...

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