SRI International's BioCyc Database Collection Expanded for Easy Access to Information about Microbes and Metabolic Pathways

MENLO PARK, Calif., Nov. 10, 2014 /PRNewswire/ -- An update to SRI International's BioCyc database collection offers mobile access and an expanded number of databases to researchers studying genomes and metabolic pathways. Researchers now have access to 5,500 genomes from all domains of life, and information about connections between genome sequences and biological function.

BioCyc 18.5 links the sequences of microbial genomes to metabolic pathways that have been rigorously curated by SRI scientists. It combines SRI's highly curated EcoCyc (E. coli encyclopedia) and MetaCyc (metabolic encyclopedia) databases, the contents of which are derived from 53,000 publications. BioCyc provides user-friendly tools for navigating, visualizing and analyzing these genome databases to yield insights for a wide range of scientific pursuits, including microbiology, biofuels research and infectious diseases.

The results from BioCyc research can lead to drug discovery, disease prevention or metabolic engineering projects in which cells are manipulated to produce a specific substance, such as an antibiotic or source of energy. BioCyc is particularly useful for helping researchers make sense of the vast amounts of data generated by "omics" (genomics, proteomics and metabolomics) studies.

In addition to including more data and new pathways, BioCyc 18.5 adds functionality that allows researchers to locate genomes of interest faster. Scientists can now search for genomes in BioCyc based on organism properties without knowing the organism's name, such as "bacteria on skin wound" or "bottom of ocean." Researchers studying metabolomics—all of the chemical compounds found in an organism—will benefit from improved capabilities for visualizing their data and how it relates to biological function.

To help speed identification of genomes that are relevant to a researcher's interests, BioCyc 18.5 contains extensive data on phenotypic properties of organisms, such as whether they are pathogenic, the range of temperatures in which they can grow and the location of where the sample was collected. The addition of extensive genome sequencing data and computationally inferred metabolic pathways in BioCyc 18.5 combines to give researchers a comprehensive understanding of any sequenced genome they are studying. 

"A key problem in post-genome biology is how to discover the functions of novel genes and pathways hiding in the thousands of microbial genomes sequenced to date," said Peter Karp, Ph.D., director of SRI International's Bioinformatics Research Group. "A new feature in BioCyc 18.5 predicts functional linkages among pairs of genes, and from those functional linkages, our software identifies potential novel pathways. A program that searches for patterns of gene co-occurrence across thousands of genomes predicts the functional linkages. The software that predicts novel pathways from the functional linkages uses computer-science methods developed for analyzing social-network data."

This new version of BioCyc includes more than 900 assembled microbial genomes from the National Institutes of Health's Human Microbiome Project, which aims to correlate changes in microbial communities in the human body with health outcomes.

"Recent discoveries point to the human microbiome as having previously unappreciated roles in human health and disease, but we have little understanding of the mechanisms," said Karp. "The metabolic reconstructions within BioCyc now provide unprecedented functional characterizations of the individual bacterial species within the human microbiome. This will aid scientists in discovering how the microbiome influences health and disease. A next step will be to produce metabolic models of the interactions among these bacteria, and of their interactions with humans."

The new BioCyc mobile app provides access to all 5,500 databases remotely, as well as access to other websites that are powered by the Pathway Tools software behind BioCyc, such as PlantCyc and MicroCyc — enabling researchers' access to data regardless of location.

Availability
Now available on the iOS in iTunes https://itunes.apple.com/us/app/ecocyc/id414535548?mt=8

About SRI International
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SOURCE SRI International