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The Incredible Shrinking Smith-Waterman


Shane Sturrock has come a long way from his job at a parrot farm. Cofounder of Edinburgh Biocomputing Systems, Sturrock, 34, developed the MPSRCH software that has recently been upgraded to allow users to run the Smith-Waterman algorithm on a desktop computer.

“Originally, we developed the software on a massively parallel supercomputer,” Sturrock says; it was funded by a human genome project grant some 10 years ago. (The name MPSRCH came from “MasPar search,” though it now stands for “microparallel search.”) At the time, a supercomputer was the only way to run the time-consuming Smith-Waterman algorithm. But when computer companies replaced 32-bit processors with 64-bits, everything changed. “Essentially, you can use a 64-bit processor as if it’s a small supercomputer,” Sturrock says.

It certainly changed things for Sturrock. That the Smith-Waterman was theoretically superior to BLAST was acknowledged in the field — SW performs a full algorithm on every single sequence while BLAST is a heuristic that saves time by rejecting the least likely sequences early on — but when one required a pricey supercomputer, the better algorithm wasn’t much of a choice. The 64-bit processors introduced the possibility that Smith-Waterman could be brought to a desktop, and suddenly a market for MPSRCH was born.

Sturrock took a sabbatical from the University of Edinburgh to start EBS last year. The company has seven employees with plans to expand sales and development.

MPSRCH, now in version four, is also growing. “The performance we’re getting [on one Alpha machine] is very close to what we were getting just a few years ago with the supercomputer,” Sturrock says. While a supercomputer can do about 1,000 million comparisons per second, Sturrock’s Alpha is doing between 600 million and 700 million.

The software can run on Silicon Graphics hardware and will soon be tested on a Sun, but EBS primarily uses Compaq Alpha machines. Is a deal in the works? Sturrock only says, “We’re having some very interesting conversations with Compaq, and they’re pointing customers our way very actively.” So far, clients include European Bioinformatics Institute and the University of Edinburgh.

Meanwhile, EBS seems to be a good place for Sturrock, who sold all his possessions at age 15 to buy his first computer. Any yearnings to return to the parrot farm? “Absolutely not,” he says.

— Meredith Salisbury


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