Collection Citation
| Collection Title | Microbial Genomics Data from the DOE Joint Genome Institute (JGI) | ||
| Collection Sponsor | USDOE - Office of Science (SC) | ||
| DOE Data Center | DOE Joint Genome Institute's (JGI) Genome Web Portal | ||
| Other Related Organizations | University of California | ||
| Main Content Type | Specialized Mix | ||
| Subject Categories | 59 - BASIC BIOLOGICAL SCIENCES | ||
| Keywords | Microbial Genomics; Microbes; Gene sequences; Gene annotation; DNA; Bacteria; Gene assemblies; BLAST | ||
| Description | The JGI makes high-quality genome sequencing data freely available to the greater scientific community through its web portal. Having played a significant role in the federally funded Human Genome Project -- generating the complete sequences of Chromosomes 5, 16, and 19--the JGI has now moved on to contributing in other critical areas of genomics research. While NIH-funded genome sequencing activities continue to emphasize human biomedical targets and applications, the JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the science mission of the Department of Energy. With efficiencies of scale established at the PGF, and capacity now exceeding three billion bases generated on a monthly basis, the JGI has tackled scores of additional genomes. These include more than 60 microbial genomes and many important multicellular organisms and communities of microbes. In partnership with other federal institutions and universities, the JGI is in the process of sequencing a frog (Xenopus tropicalis), a green alga (Chlamydomonas reinhardtii), a diatom (Thalassiosira pseudonana) , the cottonwood tree (Populus trichocarpa), and a host of agriculturally important plants and plant pathogens. Microorganisms, for example those that thrive under extreme conditions such as high acidity, radiation, and metal contamination, are of particular interest to the DOE and JGI. Investigations by JGI and its partners are shedding light on the cellular machinery of microbes and how they can be harnessed to clean up contaminated soil or water, capture carbon from the atmosphere, and produce potentially important sources of energy such as hydrogen and methane. [Excerpt from the JGI page "Who We Are" at http://www.jgi.doe.gov/whoweare/whoweare.html] From the JGI webportal users can view a photo grid of organisims, check assemblies for status, access the Integrated Microbial Genomes (IMG) system to do comparative analysis of publicly available genomes from three domains of life, access the JGI FTP directories to download data files, browse for specific collaborating scientists and institutions, use the Tree of Life navigation tool, or choose a genome and go directly to a website specific to that one genome. All of the individual sites include direct access to download sequence files, BLAST, search, view and navigate the genomic annotations. As of March 2008, The Joint Genome Institute has released 296 Prokaryotic microbial sites, with 216 in finished status. (Specialized Interface)(See also DDE00199) | ||
| DDE | DDE00201 |
