Featured Research

from universities, journals, and other organizations

Five New Metagenome Datasets Added To Joint Genome Institute Database

Date:
February 8, 2008
Source:
DOE/Joint Genome Institute
Summary:
The U.S. Department of Energy Joint Genome Institute has released an upgraded version of the IMG/M metagenome data management and analysis system. IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome DNA sequence in the context of reference isolate genomes. The new version of IMG/M includes five additional metagenome datasets generated from microbial community samples that were the subject of recently published studies.

The U.S. Department of Energy Joint Genome Institute (DOE JGI) has released an upgraded version of the IMG/M metagenome data management and analysis system. IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome DNA sequence in the context of reference isolate genomes. The new version of IMG/M includes five additional metagenome datasets generated from microbial community samples that were the subject of recently published studies.

Related Articles


These include the metagenomic and functional analysis of termite hindgut microbiota (Nature 450, 560-565, 22 November 2007) and the single cell genetic analysis of TM7, a rare and uncultivated microbe from the human mouth (PNAS, July 17, 2007, vol. 104, no. 29, 11889-11894).

IMG/M contains all isolate genomes in version 2.4 of DOE JGI’s Integrated Microbial Genomes (IMG) system, which represents an increase of 1,339 reference genomes from the previous version of IMG/M. Now, IMG/M contains 2,953 isolate genomes consisting of 819 bacterial, 50 archaeal, 40 eukaryotic genomes, and 2,044 viruses.

IMG/M provides new tools for analyzing metagenome datasets in the context of reference isolate genomes, such as the Reference Genome Context Viewer and Protein Recruitment Plot that allow the examination of metagenomes in the context of individual reference isolate genomes.

New Abundance Comparison and Functional Category Comparison tools enable pairwise function analysis (COG, Pfam, Enzyme, TIGRfam) and functional category (e.g., COG category) abundance comparisons, respectively, between a metagenome dataset and one or several reference metagenomes or genomes, and test whether the differences in abundance are statistically significant.

IMG/M has been developed jointly by the DOE JGI’s Genome Biology Program (GBP) and Lawrence Berkeley National Laboratory (LBNL) Biological Data Management and Technology Center (BDMTC). The large-scale pairwise gene similarity computations for all the genomes included in IMG/M have been carried out using ScalaBLAST by the Computational Biology and Bioinformatics Group of the Computational Sciences and Mathematics Division at Pacific Northwest National Laboratory, using the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) Molecular Sciences Computing Facility supercomputer.

The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories -- Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest -- along with the Stanford Human Genome Center to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI’s Walnut Creek, CA, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

The IMG/M datasets are available to the public at http://img.jgi.doe.gov/m.


Story Source:

The above story is based on materials provided by DOE/Joint Genome Institute. Note: Materials may be edited for content and length.


Cite This Page:

DOE/Joint Genome Institute. "Five New Metagenome Datasets Added To Joint Genome Institute Database." ScienceDaily. ScienceDaily, 8 February 2008. <www.sciencedaily.com/releases/2008/02/080208101755.htm>.
DOE/Joint Genome Institute. (2008, February 8). Five New Metagenome Datasets Added To Joint Genome Institute Database. ScienceDaily. Retrieved December 22, 2014 from www.sciencedaily.com/releases/2008/02/080208101755.htm
DOE/Joint Genome Institute. "Five New Metagenome Datasets Added To Joint Genome Institute Database." ScienceDaily. www.sciencedaily.com/releases/2008/02/080208101755.htm (accessed December 22, 2014).

Share This


More From ScienceDaily



More Plants & Animals News

Monday, December 22, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Christmas Kissing Good for Health

Christmas Kissing Good for Health

Reuters - Innovations Video Online (Dec. 22, 2014) Scientists in Amsterdam say couples transfer tens of millions of microbes when they kiss, encouraging healthy exposure to bacteria. Suzannah Butcher reports. Video provided by Reuters
Powered by NewsLook.com
Brain-Dwelling Tapeworm Reveals Genetic Secrets

Brain-Dwelling Tapeworm Reveals Genetic Secrets

Reuters - Innovations Video Online (Dec. 22, 2014) Cambridge scientists have unravelled the genetic code of a rare tapeworm that lived inside a patient's brain for at least four year. Researchers hope it will present new opportunities to diagnose and treat this invasive parasite. Matthew Stock reports. Video provided by Reuters
Powered by NewsLook.com
New Fish Species Discovered, Setting Record for World's Deepest

New Fish Species Discovered, Setting Record for World's Deepest

Buzz60 (Dec. 22, 2014) A new species of fish is discovered living five miles beneath the ocean surface, making it the deepest living fish on earth. Jen Markham has the story. Video provided by Buzz60
Powered by NewsLook.com
Earthworms Provide Cancer-Fighting Bacteria

Earthworms Provide Cancer-Fighting Bacteria

Reuters - Innovations Video Online (Dec. 21, 2014) Polish scientists isolate bacteria from earthworm intestines which they say may be used in antibiotics and cancer treatments. Suzannah Butcher reports. Video provided by Reuters
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins