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JGI Updates Microbial Metagenomics Data System

February 11, 2008
By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – The Joint Genome Institute of the US Department of Energy has released an upgraded version of its metagenomics data management and analysis system that includes five new metagenome data sets taken from recent studies.

The new data in the Integrated Microbial Genomics 2.4 system includes recent data from the functional analysis of the metagenomic sequencing of the microbiota of the termite hindgut and information from the genetic analysis of TM7, a “rare and uncultivated microbe” found in the human mouth, among others, JGI said.

The IMG/M was developed through a partnership between JGI’s Genome Biology Program and the Lawrence Berkeley National Laboratory’s Biological Data Management and Technology Center.

The system provides tools, such as the Reference Genome Context Viewer and the Protein Recruitment Plot, that are used to analyze the functional capability of microbial communities based on their metagenome DNA sequence in the context of isolate genomes. Included in the nearly 3,000 isolate reference genomes are those from more than 800 bacteria and over 2,000 viruses, as well as more than 40 eukaryotic genomes.

JGI said the gene similarity computations for the genomes were conducted using the ScalaBLAST technology from Computational Biology and Bioinformatics Group of the Pacific Northwest Laboratory, using the supercomputer at the Molecular Sciences Computing Facility.

The JGI has made the IMG/M system available here.

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