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:4/28/2016)... First quarter 2016:   , Revenues amounted to ... of 2015 The gross margin was 49% (27) ... operating margin was 40% (-13) Earnings per share rose ... was SEK 249.9 M (21.2) , Outlook   ... The operating margin for 2016 is estimated to exceed ...
(Date:4/15/2016)... -- A new partnership announced today will help life ... a fraction of the time it takes today, ... insurance policies to consumers without requiring inconvenient and ... rapid testing (A1C, Cotinine and HIV) and higi,s ... pulse, BMI, and activity data) available at local ...
(Date:3/31/2016)... 31, 2016   ... the "Company") LegacyXChange is excited to release ... soon to be launched online site for trading 100% ... ) will also provide potential shareholders a sense of ... to an industry that is notorious for fraud. The ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... - FACIT has announced the creation of a ... Propellon Therapeutics Inc. ("Propellon" or "the Company"), to ... of first-in-class WDR5 inhibitors for the treatment of ... an exciting class of therapies, possessing the potential ... patients. Substantial advances have been achieved with the ...
(Date:6/23/2016)... Prostate Cancer Foundation (PCF) is pleased to announce 24 new Young Investigator ... Members of the Class of 2016 were selected from a pool of 128 ... About the Class of 2016 PCF Young Investigators ... ... ...
(Date:6/23/2016)... ... , ... STACS DNA Inc., the sample tracking software company, today announced that ... joined STACS DNA as a Field Application Specialist. , “I am thrilled that ... of STACS DNA. “In further expanding our capacity as a scientific integrator, Hays brings ...
(Date:6/23/2016)... , June 23, 2016 ... Hematology Review, 2016;12(1):22-8 http://doi.org/10.17925/OHR.2016.12.01.22 ... , the peer-reviewed journal from touchONCOLOGY, Andrew ... escalating cost of cancer care is placing an ... result of expensive biologic therapies. With the patents ...
Breaking Biology Technology: