Navigation Links
Upgraded IMG 2.3 Data Management System released by DOE JGI to eager user community
Date:9/4/2007

WALNUT CREEK, CA -- A powerful set of computational tools established to ease the visualization and exploration of genomes flooding the public domain is now available in IMG Version 2.3 -- the Integrated Microbial Genomes (IMG) data management system hosted by the U.S. Department of Energy Joint Genome Institute (DOE JGI).

The content of IMG 2.3, upgraded with new microbial genomes from the Version 23 release of the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) collection, now includes fungi, protists (eukaryotic unicellular organisms), and plant genomes to enhance the breadth of comparative analysis. A new addition of particular interest to DOE is Pichia stipitis CBS 6054, a fungus with the exceptional capability to ferment xylose, five-carbon wood sugar, and yield high levels of ethanol.

"Using comparative approaches is a powerful means to increase our understanding of gene function," said Scott Baker, a Senior Research Scientist on the Fungal Biotechnology Team at Pacific Northwest National Laboratory. "My research is centered on fungi, so I am employing IMG 2.3 to advance our efforts to identify relevant pathways in fungi for bioenergy applications."

Baker and his colleagues, building on the pioneering work on fungal model systems that led to such biotechnology workhorses as Aspergillus niger, are currently investigating Aspergillus terreus, now incorporated in IMG 2.3, for its ability to produce itaconic acid. Products generated from itaconic acid via chemical catalysis could be used to displace petroleum-derived chemicals. This and other organic acids that can be produced by fungi and other microbes are highlighted in the DOE Energy Efficiency and Renewable Energy (EERE) Office of the Biomass Program sponsored "Top Value-Added Chemicals From Biomass" study performed jointly by PNNL and the National Renewable Energy Laboratory (http://www1.eere.energy.gov/biomass/pdfs/35523.pdf).

"Fungal genomes offer an expansive repertoire of enzymes needed for the deconstruction of plant biomass into its component sugars. The cost-effective production of cellulosic biofuels will undoubtedly involve fungal enzymes, and the ability to compare complements of enzyme families across organisms, with the tools packaged in IMG 2.3, will be essential to those researchers engaged in this effort," said Baker.

The new version of IMG contains a total of 2,878 genomes consisting of 729 bacterial, 46 archaeal, 40 eukaryotic, and 1,661 bacterial phage genomes, and 402 plasmids that did not come from a specific microbial genome sequencing project. Among these genomes, 2,609 are finished and 269 are draft genomes. IMG 2.3 contains 236 microbial genomes sequenced at DOE JGI, consisting of 157 finished and 79 draft genomes.

IMG 2.3 extensions include an expanded controlled vocabulary of IMG terms, representing over 2,300 curated product names, and a growing collection of IMG pathways that form the foundation for composite IMG networks. IMG terms, pathways, and networks are used for improving the functional characterization of genes in ongoing studies related to carbohydrate utilization, cofactor biosynthesis, and methanogenesis.

Responding to the needs of the DOE JGI user community, IMG 2.3 provides enhanced support through "MyIMG Annotations," which enables users to associate related genes of interest with their curated annotations, including product name, and enzyme number. Other user interface extensions include reorganization of the organism and gene details pages and additional genome, gene, and function search capabilities.

IMG, accessible to the public at http://img.jgi.doe.gov/, is a collaborative effort between 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 DOE JGI genomes. The next update is scheduled for December 2007.


'/>"/>

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

Related biology news :

1. GeneNotes - A novel information management software for biologists
2. Study of energy and health in Africa focuses spotlight on charcoal and forest management
3. Energy management in cells may hold key to cancer defense
4. Water management in cells
5. Aquatic plants may hold key to advancing plant disease management
6. Saharas edge studied from ground, air and space to improve water management
7. Madagascan tropical forests return thanks to better management and well-defined ownership
8. Genes In The Interferon System Important In Systemic Lupus Erythematosus
9. Fox Chase Cancer Center scientists identify immune-system mutation
10. NYU Study Reveals How Brains Immune System Fights Viral Encephalitis
11. Transport System Smuggles Medicines Into Brain
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:3/17/2016)... , March 17, 2016 ABI Research, ... forecasts the global biometrics market will reach more ... 118% increase from 2015. Consumer electronics, particularly smartphones, ... fingerprint sensors anticipated to reach two billion shipments ... Dimitrios Pavlakis , Research Analyst at ABI ...
(Date:3/11/2016)... 2016 http://www.apimages.com ) - --> ... available at AP Images ( http://www.apimages.com ) - ... to produce the new refugee identity cards. DERMALOG will be unveiling ... in Hanover next week.   --> ... used to produce the new refugee identity cards. DERMALOG will be ...
(Date:3/9/2016)... , March 9, 2016 ... identified that more than 23,000 public service employees either ... been receiving their salary unlawfully.    --> ... government identified that more than 23,000 public service employees ... had been receiving their salary unlawfully.    --> ...
Breaking Biology News(10 mins):
(Date:4/27/2016)... India , April 27, 2016 ... market research report with specific focus on US, ... Japan , to the healthcare business ... research library. Complete report on the ... 11 companies and supported with 282 tables and ...
(Date:4/26/2016)... Redwood City, CA (PRWEB) , ... April 26, ... ... company for healthcare, today announced that Ardy Arianpour has joined the company as ... 14 years of experience bringing innovative genomic technologies to market, was most recently ...
(Date:4/26/2016)... ... April 26, 2016 , ... Heidelberg Instruments, a leader ... innovation for its Volume Pattern Generator (VPG) line of lithography systems. The breakthrough ... as well as a solution for mid volume direct write lithography applications. ...
(Date:4/26/2016)... ... 2016 , ... This unique "Fertility Happy Hour" event will be held at ... get the lowdown on female fertility and the reproductive technologies that are empowering a ... Boston IVF - The Arizona Center, will give a short presentation and answer ...
Breaking Biology Technology: