A-Z Index | Phone Book | Careers

DOE JGI Extends the Capabilities of the Integrated Microbial Genome (IMG) System, Updates the IMG/M Metagenome System, Launches Education Site

September 8, 2008

David Gilbert
DOE JGI Public Affairs Manager
(925) 296-5643

WALNUT CREEK, CA—The U.S. Department of Energy Joint Genome Institute (DOE JGI) has extended the capabilities of the Integrated Microbial Genomes (IMG) data management system, updated the content of the IMG/M metagenome data management and analysis system, and has launched its educational companion site, IMG/EDU.

Version 2.6 of IMG includes new microbial genomes from Version 29 release of the National Center for Biotechnology Informations (NCBIs) Reference Sequence (RefSeq) collection. IMG 2.6 contains a total of 4,207 genomes consisting of 1078 bacterial, 56 archaeal, 40 eukaryotic genomes, 2,230 bacterial phages, and 803 plasmids that did not come from a specific microbial genome sequencing project. Among these genomes, 3,737 are finished and 470 are draft genomes. IMG 2.6 contains 308 microbial genomes sequenced at DOE JGI, consisting of 237 finished and 71 draft genomes.

IMG 2.6 includes the first version of chromosomal gene cassettes (positional gene clusters) together with estimates of their conservation across IMG genomes. The User Interface has been improved with tools for exploring gene cassettes conservation and includes additional graphical viewers for examining the functional annotation of genomes. More details on IMG 2.6 are available at: http://img.jgi.doe.gov/w/doc/releaseNotes.pdf.

The content of IMG/M, which provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence, has been updated to include three additional metagenome datasets generated from microbial community samples that were the subject of recently published studies.  These include the metagenomic and functional analysis a microbial community from Lake Washington in Seattle (Nature Biotechnology, August 2008), a hypersaline microbial mat  (Molecular System Biology 4, June 2008), and the airborne metagenome in an indoor urban environment (PLoS One 3, April 2008).

“The IMG/M system is the most comprehensive and constantly evolving resource for analyzing metagenomic data, offering an array of valuable analysis tools in conjunction with links to major public databases,” said Nature Biotechnology paper author Ludmila Chistoserdova, a microbiologist at the University of Washington.  “While very powerful, the system is user friendly and intuitive, a true ‘one-stop-shop’ for metagenomics researchers.”  More details on IMG/M are available at: http://img.jgi.doe.gov/img_mw_v241/doc/releaseNotes.pdf.

A special version of IMG, IMG/EDU, has been established to support DOE JGI's Education Program in Microbial Genome Annotation for teaching microbial genome analysis and annotation using specific microbial genomes in the comparative context of all the genomes available in IMG.

“IMG/EDU will serve as the core of a web-based portal that enables undergraduates to participate in microbial genome annotation,” said Cheryl Kerfeld, head of DOE JGI’s Education Program. “Currently, students at 12 schools nationally are using the portal in their molecular biology, genetics, microbiology and biochemistry courses in which they examine gene calls and annotate genes and biochemical pathways. By helping to build curated genomes with researchers across the globe, undergraduates will discover the concepts and applications of bioinformatics using IMG/EDU.” An additional resource, IMG/ACT, provides support for managing student classes and assignments, as well as for sharing teaching materials and guiding students in their study of gene calls and functional annotations.  

IMG, accessible to the public at http://img.jgi.doe.gov/, IMG/M, and IMG/EDU, are the result of a collaboration between the DOE JGI and Lawrence Berkeley National Laboratory Biological Data Management and Technology Center (BDMTC).

About Computing Sciences at Berkeley Lab

The Lawrence Berkeley National Laboratory (Berkeley Lab) Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy's research missions: developing new energy sources, improving energy efficiency, developing new materials and increasing our understanding of ourselves, our world and our universe.

ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 6,000 scientists at national laboratories and universities, including those at Berkeley Lab's Computational Research Division (CRD). CRD conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. NERSC and ESnet are DOE Office of Science User Facilities.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.