Starbridge’s Hypercomputing Technology applied to the Smith Waterman algorithm Searches Very Large Sets of Genetic Data in Record-Breaking Time

Salt Lake City, Utah (March 24, 2004) – Starbridge Systems®,, Inc., announced today that it is the first company to complete a full Smith Waterman comparison of the X chromosome to Y chromosome in less than five days. This data processing feat typically requires weeks or months of computation time on large clusters or custom supercomputer hardware. Starbridge accomplished the “grand challenge” task with the company’s patented Hypercomputer® hardware and a specialized implementation of the Smith Waterman pattern-matching algorithm written in Viva®, Starbridge’s powerful FPGA-programming platform.

A Smith Waterman search provides extremely accurate results, but runs more slowly than heuristic tools such as BLAST. The Starbridge Hypercomputing solution offers a compelling price/performance breakthrough—a Smith Waterman implementation that processes far larger data sets and returns significantly more detailed results than a typical BLAST search—and at significantly faster speed than today’s BLAST tools.

“Starbridge Hypercomputing now enables scientists engaged in genome scale research to use Smith Waterman as a practical tool; no longer sacrificing sensitivity for speed,” said Daniel Oswald, President and CEO of Starbridge Systems. “By applying Hypercomputing to the Smith Waterman algorithm, large scale genetic searches become inexpensive, vast amounts of new information can be discovered, and the palette of tools for serious genome research is increased.”

Other Uses for Hypercomputing

Starbridge Systems has deployed its technology for such research and development organizations as NASA, the National Security Agency, the US Air Force, universities, and supercomputer centers. Starbridge is also developing applications in partnership with TRICON Geophysics, Inc. for use in the seismic data processing market.

Starbridge Systems: The Hypercomputer Company

Utah-based Star Bridge Systems was founded in 1998 to advance reconfigurable computing technologies, creating a powerful high-performance computing platform. Compared with conventional processors, Starbridge’s scalable Hypercomputers® offer significant advantages in speed, flexibility, versatility and efficiencies of size, weight and power consumption. The Viva® development environment elevates Hypercomputers (and other field programmable gate array execution environments) into general-purpose, high performance computing systems capable of turning months into minutes for many algorithms.

For a demonstration or for more information, visit http://www.starbridgesystems.com/smithwaterman or call 801 984-4444.