GOVERNMENT

MENLO PARK, CA -- SRI International, a leading research institute based in Silicon Valley, today announced that it has used its Pathway Tools software to analyze a newly sequenced genome, Agrobacterium tumefaciens, producing a comprehensive database of its genome and computational analysis of its metabolic pathways. This database will also serve as a collaborative space where other scientists studying A. tumefaciens can share their findings. SRI researchers worked with a larger team on this project, including researchers from the University of Washington and DuPont. An article about the group's collective findings, "The Genome of Agrobacterium tumefaciens C58: Insights into the evolution and biology of a natural genetic engineer," was published in the December 14, 2001 issue of Science magazine. SRI released its A. tumefaciens database, AgroCyc, on its web site the same day (www.ecocyc.org). SRI's Pathway Tools software, which was described in a previous announcement (www.sri.com/news/releases/09-13-01.html) and article published in Science magazine (September 14, 2001), is the most sophisticated tool available for metabolic pathway analysis of a genome, a crucial component when analyzing the cellular processes that are encoded by an organism's genome. The software was able to predict A. tumefaciens' metabolic pathways, and analyzed the distribution of those pathways across its multiple chromosomes. The AgroCyc database is the twelfth in SRI's growing collection of pathway/genome databases. Additional new databases include those for Pseudomonas aeruginosa and the result of a joint effort with Stanford University sponsored by the Department of Energy's Microbial Cell Project, Caulobacter crescentus. The software provides an environment for publishing pathway/genome databases on the web, and is the first software environment that can create model-organism databases for many different organisms. SRI's Pathway Tools is the only software of its kind that is in active use by scientists who were not involved in its development. "Pathway analysis reduces the cognitive complexity of a genome by allowing scientists to think about the biochemical network of an organism in larger units of organization -- in terms of pathways rather than individual gene products," said Dr. Peter Karp, Director of SRI International's Bioinformatics Research Group. "The Pathway Tools software identified the metabolic roles of 709 Agrobacterium enzymes in 178 metabolic pathways." Pathway Tools encodes large and complex scientific theories that are the basis of systems biology, the complex interactions between all levels of biological information -- genomic DNA, and informational pathways and networks. Management of these theories leads to a greater understanding of biological systems, improved scientific collaboration, and more rapid integration of disparate sources of bioscience knowledge. SRI's Bioinformatics Research Group: SRI International's Bioinformatics Research Group performs interdisciplinary research at the intersection of computer science and molecular biology. Its objectives are to develop software and database tools that advance genomics, while addressing fundamental research problems in bioinformatics.