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Latest Integrated Microbial Genomes (IMG) Data Management System Update Release
December 06, 2007DOE Joint Genome Institute to Host September IMG Workshop
WALNUT CREEK, CA--Version 2.4 of the Integrated Microbial Genomes (IMG) data management system, a resource provided to the scientific community for microbial genome data analysis, has now been released. Hosted by the U.S. Department of Energy Joint Genome Institute (DOE JGI), IMG has built a popular following as reflected in the overwhelming response to IMG workshops offered in Spring 2008, now full. DOE JGI has added a fall session, September 15-19, 2008. Registration is now open at http://www.jgi.doe.gov/meetings/mgm/.
IMG 2.4's content has been updated with new microbial genomes from the Version 25 release of the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq). IMG 2.4 also contains a total of 3,637 genomes consisting of 818 bacterial, 50 archaeal, and 40 eukaryotic genomes; 2,042 viruses and bacterial phages; and 687 plasmids. Among these genomes, there are 3,334 finished and 303 draft genomes, of which 256 (185 finished and 71 draft) are genomes sequenced by DOE JGI.
The IMG native controlled vocabulary of functional terms and pathways has been extended to 4,148 terms and 524 pathways, with 546,169 genes characterized using IMG terms. Functional annotation of genomes in IMG has been further enhanced through the computation of fused genes and by filling in various RNA genes missing from the original genome data sets.
IMG's user interface has been reorganized and enhanced to improve ease of use. IMG's user manual, UsingIMG, has been revised and extended. For more details, see What's New (and Using IMG at http://img.jgi.doe.gov/.
IMG 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 IMG update is scheduled for March, 2008.
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.
DOE Joint Genome Institute
The IMG native controlled vocabulary of functional terms and pathways has been extended to 4,148 terms and 524 pathways, with 546,169 genes characterized using IMG terms. Functional annotation of genomes in IMG has been further enhanced through the computation of fused genes and by filling in various RNA genes missing from the original genome data sets.
IMG's user interface has been reorganized and enhanced to improve ease of use. IMG's user manual, UsingIMG, has been revised and extended. For more details, see What's New (and Using IMG at http://img.jgi.doe.gov/.
IMG 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 IMG update is scheduled for March, 2008.
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.
DOE Joint Genome Institute
Microbial Genome Current Events and Microbial Genome News RSSNew genomic model defines microbes by diet -- provides tool for tracking environmental change
In line with the U.S. Department of Energy (DOE) interest in characterizing the biotic factors involved in global carbon cycling, the DOE Joint Genome Institute (JGI) characterizes a diverse array of plants, microorganisms, and the communities in which they reside to inform options for reducing and stabilizing atmospheric greenhouse gases.
NC State Researchers Get to Root of Nematode Genome
North Carolina State University scientists and colleagues have completed the genome sequence and genetic map of one of the world's most common and destructive plant parasites - Meloidogyne hapla, a microscopic, soil-dwelling worm known more commonly as the northern root-knot nematode.
BGSU undergraduates to pilot groundbreaking genome project
Bowling Green State University biology undergraduates will soon be contributing to the body of knowledge in genomics while they learn. The University has been selected as one of 12 institutions nationwide to pilot the new Microbial Genome Annotation research program through the U.S. Department of Energy Joint Genome Institute (DOE JGI).
Massive reanalysis of genome data solves case of the lethal genes
It is better to be looked over than overlooked, Mae West supposedly said. These are words of wisdom for genome data-miners of today.
Scientists expand microbe 'gene language'
An international group of scientists has expanded the universal language for the genes of both disease-causing and beneficial microbes and their hosts.
DOE JGI Finishes 100th Microbial Genome
Microbes, thriving in even the world's most extreme environments, are capable of performing myriad biological functions, learned over the billions of years they have inhabited the planet.
DOE JGI releases experimental metagenomics data management & analysis system
To tackle the computational challenges of analyzing the complex world of microbial communities, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has released to the worldwide research community IMG/M, an experimental metagenome data management and analysis system.
Virginia Bioinformatics Institute launches microbial database
Researchers at the Virginia Bioinformatics Institute at Virginia Tech have launched a publicly-available microbial database to host a range of microbial genome sequences.
Sequencing our seas
Scientists have sequenced and compared the genomes of planktonic microbes living throughout the water column in the Pacific Ocean.
Poison + water = hydrogen. New microbial genome shows how
Take a pot of scalding water, remove all the oxygen, mix in a bit of poisonous carbon monoxide, and add a pinch of hydrogen gas. It sounds like a recipe for a witch's brew. It may be, but it is also the preferred environment for a microbe known as Carboxydothermus hydrogenoformans.
More Microbial Genome Current Events and Microbial Genome News Articles
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The Microbial Models of Molecular Biology: From Genes to Genomes by Rowland H. Davis (Author) Univ. of California, Irvine. Provides an historical account of molecular biology, focusing on the microorganisms used, how they were chosen, what they contributed, and how they were displaced by others. Examines the introduction of microbial model organisms from 1925 to present time and explores the rise of genetics and molecular biology. DNLM: Genetics, Microbial--history. |
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Microbial Gene Essentiality: Protocols and Bioinformatics (Methods in Molecular Biology) by Andrei L. Osterman (Editor), Svetlana Y. Gerdes (Editor) This book contains a comprehensive collection of experimental and computational strategies and techniques for microbial genome-scale essentiality studies, developed and presented by the leading groups in the field. In addition to wet-lab protocols, the book describes statistical methods essential for planning successful large-scale essentiality screens, as well for data evaluation and analysis; in-silico prediction of gene essentiality using genome-scale reconstructed metabolic models; and data integration and comparative analysis in the context of genomic databases. All protocols follow the successful "Methods in Molecular Biology" series format, each offering an introduction outlining the principles behind the techniques, step-by-step instructions, lists of the necessary equipment and... | |
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Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists (Computational Biology) by David W. Ussery (Author), Trudy M. Wassenaar (Author), Stefano Borini (Author) The major difficulty many microbiologists face is simply that of too much information. As a result of sequencing technologies becoming so economical, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. This accessible text/reference provides a coherent set of tools and a methodological framework for comparing raw DNA sequences and fully annotated genome sequences, then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Easy-to-follow, this introductory textbook is built around teaching computational / bioinformatics methods for comparison of microbial genomes, and includes detailed examples of how to compare them at the level of DNA,... |
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Bioinformatic Tools for the Analysis of Microbial Genomes (Comprehensive Summaries of Uppsala Dissertations, 510) by Thomas Sicheritz Ponten (Author) | |
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Genome-based Methods.(Techniques of classic microbial genetics are used to identify and characterize the function of selected genes regulated by a particular ... An article from: Food Ingredient News by Business Communications Company, Inc. (Publisher) This digital document is an article from Food Ingredient News, published by Business Communications Company, Inc. on November 1, 2004. The length of the article is 518 words. The page length shown above is based on a typical 300-word page. The article is delivered in HTML format and is available in your Amazon.com Digital Locker immediately after purchase. You can view it with any web browser. Citation Details Title: Genome-based Methods.(Techniques of classic microbial genetics are used to identify and characterize the function of selected genes regulated by a particular stress response) Publication: Food Ingredient News (Newsletter) Date: November 1, 2004 Publisher: Business Communications Company, Inc. Volume: 12 Issue: 11 Page: NA Distributed by Thomson... | |
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Battle of the Genomes: The Struggle for Survival in a Microbial World.(Book review): An article from: Emerging Infectious Diseases by Marta Gwinn (Author) This digital document is an article from Emerging Infectious Diseases, published by Thomson Gale on June 1, 2007. The length of the article is 577 words. The page length shown above is based on a typical 300-word page. The article is delivered in HTML format and is available in your Amazon.com Digital Locker immediately after purchase. You can view it with any web browser. Citation Details Title: Battle of the Genomes: The Struggle for Survival in a Microbial World.(Book review) Author: Marta Gwinn Publication: Emerging Infectious Diseases (Magazine/Journal) Date: June 1, 2007 Publisher: Thomson Gale Volume: 13 Issue: 6 Page: 959(2) Article Type: Book review Distributed by Thomson... | |
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Microbial Pathogenomics (Genome Dynamics) by H. De Reuse (Editor), S. Bereswill (Editor) |
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Microbial Genome Methods by Kenneth W. Adolph (Author) Learn to apply powerful molecular biology and genetics techniques to your microbial research with this easy-to-understand, practical guide. Microbial Genome Methods distills complex experimental procedures into fundamental techniques that can be readily adapted to your own research. In addition, this book provides background information specifically relevant to microbial research, as well as descriptions of expected results.The book is divided into two sections. Section one covers eukaryotic microbes, with emphasis on the yeast Saccharomyces cerevisiae. Section two covers prokaryotic microbes, focusing on Escherichia coli, and other important bacteria. These microbes were selected because they are widely studied and understood, but all information can be easily applied to the microbe you... |
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Microbial Genomes (Infectious Disease) by Claire M. Fraser (Editor), Timothy Read (Editor), Karen E. Nelson (Editor) The Institute for Genomic Research, Rockville, MD. Describes some of the most common computational methods and their applications for studying pathogenic microrganisms. Also discusses issues relevant to the reconstruction of metabolic pathways, cell cycle processes, microbial evolution, and more. DNLM: Bacteria--genetics. |
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Battle of the Genomes: The Struggle for Survival in a Microbial World by H. M. Lachman (Author) This book is an account of some of the most malignant infectious microbes encountered by humans and the genetic disorders they spawned. It's also a tale of how scientific progress over the past 150 years is giving man the tools to fight back. |
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