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DOE JGI releases IMG 1.5 with curated archaeal genomes
June 28, 2006WALNUT CREEK, CA—Version 1.5 of the Integrated Microbial Genomes (IMG) data management system of the U.S. Department of Energy Joint Genome Institute (DOE JGI) has been released to the public. IMG 1.5 now contains a total of 741 genomes (435 bacterial, 32 archaeal, 15 eukaryotic genomes and 259 bacterial phages) of which 602 are finished and 139 are draft genomes.
IMG 1.5 contains 62 finished and 100 draft genomes sequenced by DOE JGI, bringing this total to 162 microbial genomes generated in-house. Compared to the previous release, IMG 1.5 contains 38 new (17 finished, 21 draft) DOE JGI genomes and 21 new public microbial genomes.
Among the challenges in genomics remains the determination of the precise location of genes from DNA sequence information. DOE JGI has embarked on curating the gene models of microbial genomes culled from public sources. Towards this goal, IMG 1.5 now contains 22 archaeal genomes with curated gene models and detailed documentation of the methodology and standards employed for achieving this goal. A separate IMG Curated Archaeal Genomes data mart (http://img.jgi.doe.gov/archaeal_qa/) contains these genomes with their corresponding original genomes from the public domain, and allows the examination of gene model changes by comparing each curated gene model with the original.
IMG 1.5 extensions include the addition of IMG terms (which are curated protein products) and IMG pathways to characterize genes. Also, users are now able to enter their own product name for a gene directly through the gene details page and to propagate this annotation to selected paralogs, orthologs, and homologs of the gene. User interface extensions include such enhanced comparative analysis capabilities as gene profiles across genomes. For more details on the user interface, see What's New ( http://img.jgi.doe.gov/pub/doc/releaseNotes.html ).
DOE/Joint Genome Institute
IMG 1.5 extensions include the addition of IMG terms (which are curated protein products) and IMG pathways to characterize genes. Also, users are now able to enter their own product name for a gene directly through the gene details page and to propagate this annotation to selected paralogs, orthologs, and homologs of the gene. User interface extensions include such enhanced comparative analysis capabilities as gene profiles across genomes. For more details on the user interface, see What's New ( http://img.jgi.doe.gov/pub/doc/releaseNotes.html ).
DOE/Joint Genome Institute
Genome Current Events and Genome News RSSTime of day matters to thirsty trees, U of T researcher discovers
The time of day matters to forest trees dealing with drought, according to a new paper produced by a research team led by Professor Malcolm Campbell, University of Toronto Scarborough's vice-principal for research and colleagues in the department of cell and systems biology at the St. George campus.
Genetic analysis helps dissect molecular basis of cardiovascular disease
Using highly precise measurements of plasma lipoprotein concentrations determined by nuclear magnetic resonance spectroscopy (NMR), researchers led by Daniel Chasman at Brigham and Women's Hospital and Harvard Medical School in Boston, MA, the Framingham Heart Study in Framingham, and the PROCARDIS consortium in Stockholm, Sweden and Oxford, England performed genetic association analysis across the whole genome among 17,296 women of European ancestry from the Women's Genome Health Study.
Gene mismatch influences success of bone marrow transplants
A commonly inherited gene deletion can increase the likelihood of immune complications following bone marrow transplantation, an international team of researchers reports in the November 22 advance online issue of Nature Genetics.
Scientists at UA, collaborating institutions decode maize genome
Scientists from the University of Arizona led by Arizona Genomics Institute director Rod A. Wing and from collaborating institutions have deciphered the complete genetic code of the maize plant for the first time.
Ancestry attracts, but love is blind
People preferentially marry those with similar ancestry, but their decisions are not necessarily based on hair, eye or skin colour.
WPI Researchers Take Aim at Hard-to-Treat Fungal Infections
A team of researchers at the Worcester Polytechnic Institute (WPI) Life Sciences and Bioengineering Center at Gateway Park has developed a new model system to study fungal infections.
Technique finds gene regulatory sites without knowledge of regulators
A new statistical technique developed by researchers at the University of Illinois allows scientists to scan a genome for specific gene-regulatory regions without requiring prior knowledge of the relevant transcription factors.
Causative gene of a rare disorder discovered by sequencing only protein-coding regions of genome
For the first time, scientists have successfully used a method called exome sequencing to quickly discover a previously unknown gene responsible for a mendelian disorder.
New research into the mechanisms of gene regulation
A team led by Penn State's Ross Hardison, T. Ming Chu Professor of Biochemistry and Molecular Biology, has taken a large step toward unraveling how regulatory proteins control the production of gene products during development and growth.
Maize cell wall genes identified, giving boost to biofuel research
Purdue University scientists have helped identify and group the genes thought to be responsible for cell wall development in maize, an effort that expands their ability to discover ways to produce the biomass best suited for biofuels production.
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