WALNUT CREEK, CA–Version 1.5 of the Integrated Microbial Genomes (IMG) data management system of the U.S. Department of Energy Joint Genome Institute (DOE JGI) has been released to the public. IMG 1.5 now contains a total of 741 genomes (435 bacterial, 32 archaeal, 15 eukaryotic genomes and 259 bacterial phages) of which 602 are finished and 139 are draft genomes.
IMG 1.5 contains 62 finished and 100 draft genomes sequenced by DOE JGI, bringing this total to 162 microbial genomes generated in-house. Compared to the previous release, IMG 1.5 contains 38 new (17 finished, 21 draft) DOE JGI genomes and 21 new public microbial genomes.
Among the challenges in genomics remains the determination of the precise location of genes from DNA sequence information. DOE JGI has embarked on curating the gene models of microbial genomes culled from public sources. Towards this goal, IMG 1.5 now contains 22 archaeal genomes with curated gene models and detailed documentation of the methodology and standards employed for achieving this goal. A separate IMG Curated Archaeal Genomes data mart ) contains these genomes with their corresponding original genomes from the public domain, and allows the examination of gene model changes by comparing each curated gene model with the original.
IMG 1.5 extensions include the addition of IMG terms (which are curated protein products) and IMG pathways to characterize genes. Also, users are now able to enter their own product name for a gene directly through the gene details page and to propagate this annotation to selected paralogs, orthologs, and homologs of the gene. User interface extensions include such enhanced comparative analysis capabilities as gene profiles across genomes. For more details on the user interface, see What’s New ).
IMG, accessible to the public at http://img.archive.jgi.doe.gov/, is the result of a collaboration between the DOE JGI and the Lawrence Berkeley National Laboratory Biological Data Management and Technology Center (BDMTC). IMG is updated on a quarterly basis with new public and JGI genomes. The next update is scheduled for September 1, 2006.
The DOE Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five 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 mission related to clean energy generation and environmental characterization and clean-up. 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.
The LBNL Biological Data Management and Technology Center (BDMTC) ) has expertise in the development of biological data management systems and bioinformatics tools. BDMTC is collaborating with DOE JGI on the development and maintenance of IMG (http://img.archive.jgi.doe.gov) and IMG/M (http://img.archive.jgi.doe.gov/m).