Bioinformatics Tools for Renewable Energy Research

genome fragment
Representation of a genome fragment.
SRI International

SRI International, an independent nonprofit research and development organization, has been awarded a grant by the Department of Energy (DOE) to expand its MetaCyc database and enhance its Pathway Tools software. This project will give SRI’s bioinformatics tools even greater utility in the emerging area of bioenergy, or renewable energy derived from biological sources.

SRI will expand its MetaCyc database to include energy-related metabolic pathways and enzymes associated with lignocellulosic biomass degradation, hydrogen production, and microalgae oil production. This expansion will allow the Pathway Tools software to recognize bioenergy-related pathways in sequenced microbes, resulting in more accurate metabolic pathway reconstructions, and enabling scientists to develop new ways to produce fuel and other valuable products from biomass and microorganisms.

“Expanding our use of renewable energy resources, such as biomass, is currently a major challenge facing society,” said Peter Karp, Ph.D., director, Bioinformatics Research Group in the Artificial Intelligence Center at SRI. “Designing optimal new pathways for desired chemical products, such as biofuels, is a challenging problem for metabolic engineers because of the huge space of potential pathways that must be explored. This area is ripe for improved computational approaches.”

Pathway Tools software will draw on data in SRI’s databases to generate alternative pathways to create a target compound from specified feedstocks. SRI’s software will also evaluate each pathway’s utility to produce the specified target compounds, thereby allowing researchers to quickly identify and evaluate multiple pathways, design effective research protocols, and shorten development timeframes.

More than 2,000 researchers in government, academia, and industry already use SRI’s bioinformatics databases and software tools to accelerate research leading to advances in biotechnology, including the development of new drugs and new routes to important chemicals.

MetaCyc, a database in SRI’s BioCyc database collection, is the largest database of experimentally determined and literature-curated metabolic pathways available. Pathway Tools is a collection of software tools that predicts the metabolic pathways of organisms from their sequenced genomes and generates organism-specific pathway databases by comparing the genome annotation of each organism to the pathways within the MetaCyc database. The software also helps researchers query, visualize, analyze, and curate pathway databases. BioCyc is a collection of such pathway databases.

BioCyc databases are freely available to all researchers. Pathway Tools software is freely available to academics for research purposes.

Read Biofuels and Bioenergy: Processes and Technologies from Amazon.

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