NCBI’s Virus Variation Resource Enhancements Include Standardized Search Criteria


NCBI’s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses – no more stumbling through multiple synonyms to find what you need. Now you can search using standardized biological criteria and intuitive pull-down menus.

Virus Variation Homepage

Figure 1. The Virus Variation Resource homepage. Modules for seven viral groups are at the top of the page.

Virus Variation has modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A, and Zika virus. These modules now include a variety of new enhancements:

  • Search for sequences based on standardized gene and protein names as well as standardized sample information like host and isolation source.
  • Generate standardized custom labels when downloading and analyzing sequences in multiple sequence alignments and trees.
  • Limit sequence searches to full-length proteins and/or complete gene/protein sets.
  • Collapse identical sequences and use a single sequence to represent them in downloads and analyses.

These updates were published in a recent paper in Nucleic Acids Research: Hatcher EL, Zhdanov SA, Bao Y, Blinkova O, Nawrocki EP, Ostapchuck Y, Schäffer AA, Brister JR. Virus Variation Resource – improved response to emergent viral outbreaks. Nucleic Acids Res. 2017 Jan 4;45(D1):D482-D490. doi: 10.1093/nar/gkw1065. Epub 2016 Nov 28. (https://www.ncbi.nlm.nih.gov/pubmed/27899678).

Finally, the Virus Variation resource also incorporates an improved tree viewer. Now you can locate individual isolates and highlight branches on phylogenetic or cluster trees using standardized metadata terms and other search criteria.

virus variation Tree viewer

Figure 2. The improved tree viewer.

To learn more about updated features and how to use them, please see the Variation help page.

Please stay tuned as new annotation pipelines will soon be available for several viruses.

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