Navigation Links
DOE JGI extends the capabilities of the Integrated Microbial Genome System
Date:9/8/2008

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).


'/>"/>

Contact: David Gilbert
degilbert@lbl.gov
925-296-5643
DOE/Joint Genome Institute
Source:Eurekalert

Related biology news :

1. Successful cooperation extends Dragon Program
2. Thinking makes it so: Science extends reach of prosthetic arms
3. Genome of simplest animal reveals ancient lineage, confounding array of complex capabilities
4. Green roofs differ in building cooling, water handling capabilities
5. Argonne-University of Chicago joint venture bolsters genomic sequencing capabilities
6. bioMETRX Expands Engineering and Manufacturing Capabilities
7. Lean and mean biomass-degrading fungus reveals capabilities for improved biofuel production
8. Integrated Fuel Technologies gets worldwide license for Argonne-developed Diesel DeNOx Catalyst
9. Latest Integrated Microbial Genomes data management system update release
10. Antimicrobial sutures reduce infections in brain shunt surgery, study finds
11. Barren seafloor teeming with microbial life
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/9/2016)...  Perkotek an innovation leader in attendance control systems is proud to announce the ... employers to make sure the right employees are actually signing in, and to even ... ... ... ...
(Date:6/7/2016)... TORONTO , June 7, 2016  Syngrafii ... begun a business relationship that includes integrating Syngrafii,s ... pilot branch project. This collaboration will result in ... for the credit union, while maintaining existing document ... http://photos.prnewswire.com/prnh/20160606/375871LOGO ...
(Date:6/2/2016)... The Department of Transport Management (DOTM) ... million US Dollar project, for the , Supply ... Enrolment, and IT Infrastructure , to ... implementation of Identity Management Solutions. Numerous renowned international vendors participated ... was selected for the most compliant and innovative ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... Calif. , June 23, 2016  Blueprint Bio, ... biological discoveries to the medical community, has closed its ... Matthew Nunez . "We have received ... with the capital we need to meet our current ... essentially provide us the runway to complete validation on ...
(Date:6/23/2016)... June 23, 2016 On Wednesday, June ... 4,833.32, down 0.22%; the Dow Jones Industrial Average edged 0.27% ... at 2,085.45, down 0.17%. Stock-Callers.com has initiated coverage on the ... Nektar Therapeutics (NASDAQ: NKTR ), Aralez Pharmaceuticals Inc. ... BIND ). Learn more about these stocks by ...
(Date:6/23/2016)... WI (PRWEB) , ... June 23, 2016 , ... ... focused on quality, regulatory and technical consulting, provides a free webinar ... presented on July 13, 2016 at 12pm CT at no charge. , Incomplete ...
(Date:6/23/2016)... SAN FRANCISCO , June 22, 2016  Amgen ... platinum sponsorship of the QB3@953 life sciences ... improve human health. The shared laboratory space at QB3@953 ... startups overcome a key obstacle for many early stage ... As part of the sponsorship, Amgen launched two "Amgen ...
Breaking Biology Technology: