Database Commons a catalog of biological databases

Database Commons - Virus Variation

Virus Variation

Citations: 21

z-index 1.78

Short name Virus Variation
Full name Virus Variation
Description Retrieve,analyze,and download viral sequences from a value added database using a specialized search interface.
URL http://www.ncbi.nlm.nih.gov/genome/viruses/variation/
Year founded 2013
Last update & version 2016-07-10    v1.0
Availability Free to all users
University/Institution hosted National Center for Biotechnology Information
Address 10 Center Dr, Bethesda, MD 20892USA
City Bethesda
Province/State MD
Country/Region United States
Contact name J. Rodney Brister
Contact email jamesbr@ncbi.nlm.nih.gov
Data type(s)
Major organism(s)
Keyword(s)
  • variation
  • viral sequence
Publication(s)
  • Virus Variation Resource - improved response to emergent viral outbreaks. [PMID: 27899678]

    Eneida L Hatcher, Sergey A Zhdanov, Yiming Bao, Olga Blinkova, Eric P Nawrocki, Yuri Ostapchuck, Alejandro A Schäffer, J Rodney Brister
    Nucleic acids research 2017:45(D1)
    0 Citations (Google Scholar as of 2017-02-16)

    Abstract: The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource is located at http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A and Zika virus Each module is supported by pipelines that scan newly released GenBank records, annotate genes and proteins and parse sample descriptors and then map them to controlled vocabulary. These processes in turn support a purpose-built search interface where users can select sequences based on standardized gene, protein and metadata terms. Once sequences are selected, a suite of tools for downloading data, multi-sequence alignment and tree building supports a variety of user directed activities. This manuscript describes a series of features and functionalities recently added to the Virus Variation Resource. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  • Virus Variation Resource--recent updates and future directions. [PMID: 24304891]

    J Rodney Brister, Yiming Bao, Sergey A Zhdanov, Yuri Ostapchuck, Vyacheslav Chetvernin, Boris Kiryutin, Leonid Zaslavsky, Michael Kimelman, Tatiana A Tatusova
    Nucleic acids research 2014:42(Database issue)
    21 Citations (Google Scholar as of 2017-02-16)

    Abstract: Virus Variation (http://www.ncbi.nlm.nih.gov/genomes/VirusVariation/) is a comprehensive, web-based resource designed to support the retrieval and display of large virus sequence datasets. The resource includes a value added database, a specialized search interface and a suite of sequence data displays. Virus-specific sequence annotation and database loading pipelines produce consistent protein and gene annotation and capture sequence descriptors from sequence records then map these metadata to a controlled vocabulary. The database supports a metadata driven, web-based search interface where sequences can be selected using a variety of biological and clinical criteria. Retrieved sequences can then be downloaded in a variety of formats or analyzed using a suite of tools and displays. Over the past 2 years, the pre-existing influenza and Dengue virus resources have been combined into a single construct and West Nile virus added to the resultant resource. A number of improvements were incorporated into the sequence annotation and database loading pipelines, and the virus-specific search interfaces were updated to support more advanced functions. Several new features have also been added to the sequence download options, and a new multiple sequence alignment viewer has been incorporated into the resource tool set. Together these enhancements should support enhanced usability and the inclusion of new viruses in the future.

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Tags

DNA
Viroid/virus
variation viral sequence

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Shixiang Sun [2017-02-16]
    • Lina Ma [2016-04-08]
    • Hongyan Yin [2016-03-31]
    • Mengwei Li [2016-02-15]
    • Jian Sang [2015-07-01]
    • Hongyan Yin [2015-06-26]
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