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The genome portal of the Department of Energy Joint Genome Institute: 2014 updates.

• The genome portal of the Department of Energy Joint Genome Institute: 2014 updates.
  Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I, Smirnova T, Grigoriev IV, Dubchak I.
  Nucleic Acids Res. 2014,42(1):D26-31.
  

Abstract

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (https://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Here we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

The Genome Portal of the Department of Energy Joint Genome Institute

• The Genome Portal of the Department of Energy Joint Genome Institute
  Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I.
  Nucleic Acids Res. 2012 Jan;40(Database issue):D26-32.

Abstract

The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (https://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. We describe here the general organization of the Genome Portal and the most recent addition, MycoCosm (http://jgi.doe.gov/fungi), a new integrated fungal genomics resource.