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:11/16/2016)... 2016 Sensory Inc ., a ... for consumer electronics, and VeriTran , a ... industry, today announced a global partnership that will ... authenticate users of mobile banking and mobile payments ... software which requires no specialized biometric scanners, yet ...
(Date:11/14/2016)... Inc. ("xG" or the "Company") (Nasdaq: XGTI, XGTIW), a ... challenging operating environments, announced its results for the third ... conference call to discuss these results on November 15, ... Key Recent Accomplishments The ... Vislink Communication Systems. The purchase is expected to close ...
(Date:6/22/2016)... , June 22, 2016  The American College of Medical ... Show Executive Magazine as one of the fastest-growing trade ... 25-27 at the Bellagio in Las Vegas ... highest percentage of growth in each of the following categories: ... companies and number of attendees. The 2015 ACMG Annual Meeting ...
Breaking Biology News(10 mins):
(Date:12/8/2016)... DIEGO , Dec. 8, 2016  Renova™ ... for congestive heart failure and type 2 diabetes, ... for a novel adeno-associated virus (AAV) vector developed ... , M.D., Ph.D., at Stanford University. The company ... its paracrine gene therapy product pipeline. ...
(Date:12/8/2016)... 8, 2016 Oxford Gene Technology ... SureSeq™ NGS panel range with the launch of the SureSeq ... study of variants in familial hypercholesterolemia (FH). The panel delivers ... on a single small panel and allows customisation by ,mix ... all exons for LDLR , P C ...
(Date:12/8/2016)... (PRWEB) , ... December 08, 2016 , ... This CAST ... approvals for biotech crops. The authors focus on the economic effects in countries that ... approval of new biotech crops and the resultant risk of low level presence (LLP) ...
(Date:12/8/2016)... SEOUL, South Korea , Dec. 8, 2016 /PRNewswire/ ... completed a $21 billion KRW (US $18.9M) Series A ... Management, Kolon Investment, G.N. Tech Venture and SNU Bio ... by Eutilex to 30.5 billion KRW (US $27.7M) since ... will help Eutilex to bolster the development and commercialization ...
Breaking Biology Technology: