WALNUT CREEK, Calif.— 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 Information's (NCBI's) 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 (http://www.jgi.doe.gov/education/genomeannotation.html) 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 (http://jgi.doe.gov/education/annotation_tools.html), 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, (http://img.jgi.doe.gov/m), and IMG/EDU (http://img.jgi.doe.gov/edu), are the result of a collaboration between the DOE JGI and Lawrence Berkeley National Laboratory Biological Data Management and Technology Center (BDMTC).
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five DOE national laboratories -- Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest -- along with the Stanford Human Genome Center to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI's Walnut Creek, Calif., Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Additional information about DOE JGI can be found at: http://www.jgi.doe.gov/.