In an initial demonstration project, scientists doing research at the NCI's Advanced Biomedical Computing Center in Frederick, Maryland, produced a comprehensive map of short tandem repeat sequences (STRs), often used as gene markers, for the entire human genome. Using the Cray SV1 supercomputer located at the NCI, computations that previously took hours are being completed in seconds. This will enable biologists to do full-scale analyses which previously were impractical, according to the Cray officials.
"In preliminary testing, the unique technologies available on Cray vector supercomputers have provided enormous speed-ups for full-scale analysis of some common types of bioinformatics problems", stated Bill Long, Cray's chief collaborator for the NCI work. "If we assume that this validation continues, we believe there is a potential to make full-scale, exhaustive analysis of many bioinformatics problems feasible for the first time." Although exhaustive analysis typically produces results that are more complete and reliable than methods based on statistical sampling, as Mr. Long noted, to date exhaustive analysis has been too slow and expensive to use routinely.
The short tandem repeats, equally known as micro-satellites, are repetitive sequences of DNA that scientists have exploited for several years as tools to map new genes, study the structure of chromosomes, and compare the DNA of different species, all of which are major areas of interest in biology and medical research. Other bioinformatics software tools under development in the NCI-Cray collaboration include EST cluster assembly, genome assembly from BAC clones, non-tandem repeats, CG island detection, single nucleotide polymorphism (SNP) analysis, and the extension to protein sequences for proteomic applications.
The NCI's Advanced Biomedical Computing Center serves 1800 biological researchers worldwide. Using a Cray supercomputer, this Center played a critical role in solving the 3D structure of HIV-1 protease, an enzyme which HIV utilises to infect human immune cells. With the 3D structure clarified, scientists were able to design highly effective protease inhibitors which are now the mainstay of AIDS therapy. For this work, the Advanced Biomedical Computing Center was named a finalist for the prestigious Computerworld Smithsonian science award in 2000.
Cray Inc. designs, builds and sells high-performance MPP or Massive Parallel Processors, vector processor and general-purpose parallel computer systems. The company manages leading edge technology, multiple product platforms, nearly 900 employees, a worldwide installed base of supercomputer systems, major manufacturing and service capabilities, and extensive global customer relationships. Cray believes its Multithreaded Architecture and Cray T3E, Cray SuperCluster, and Cray SV2 systems together represent the future of supercomputing.