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Research Project: INTERVENTION STRATEGIES TO CONTROL VIRAL DISEASES OF SWINE

Location: Virus and Prion Research

Title: Influenza research database: an integrated bioinformatics resource for influenza virus research

Author
item ZHANG, YUN - J. CRAIG VENTER INSTITUTE
item AEVERMANN, BRIAN - J. CRAIG VENTER INSTITUTE
item Anderson, Tavis
item BURKE, DAVID - UNIVERSITY OF CAMBRIDGE
item DAUPHIN, GWENAELLE - FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS (FAO)
item GU, ZHIPING - COLLABORATOR
item HE, SHERRY - COLLABORATOR
item KUMAR, SANJEEV - COLLABORATOR
item LARSEN, CHRISTOPHER - COLLABORATOR
item LEE, ALEXANDRA - J. CRAIG VENTER INSTITUTE
item Vincent, Amy

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2016
Publication Date: 1/4/2017
Citation: Zhang, Y., Aevermann, B., Anderson, T.K., Burke, D.F., Dauphin, G., Gu, Z., He, S., Kumar, S., Larsen, C.N., Lee, A.J., Li, X., Macken, C., Mahaffey, C., Pickett, B.E., Reardon, B., Smith, T., Stewart, L., Suloway, C., Sun, G., Tong, L., Vincent, A.L., Walters, B., Zaremba, S., Zhao, H., Zhou, L., Zmasek, C., Klem, E.B., Scheuermann, R.H. 2017. Influenza research database: an integrated bioinformatics resource for influenza virus research. Nucleic Acids Research. 45(D1):D466-D474. doi:10.1093/nar/gkw857.

Interpretive Summary: Understanding how influenza A viruses (IAV) are changing and how this varies between regions is critical to reduce disease burden. Global IAV surveillance programs and regional investigator efforts tracking genetic change has created a prodigious amount of data. For example, there are over 100,000 hemagglutinin (HA) sequences on publicly available websites. The Influenza Research Database (IRD) was founded to facilitate the analysis of these data and enhance research and development of vaccines, diagnostics, and therapeutics against IAV. IRD achieves this by providing a comprehensive collection of influenza-related data, analytical tools that allow for the visualization and description of IAV genetic diversity, custom algorithms that predict novel proteins, nomenclature tools for the automatic identification of HA type and HA subtype numbering, phenotypic annotations of sequences, and a centralized location for information on disease events and host factor and antiviral drug information. This resource will aid and improve agricultural production and pandemic preparedness by acting as a repository for all IAV data, and its user-friendly analytical and visualization tools when applied to these data can identify important genetic changes in IAV facilitating vaccine and diagnostic updates for use in swine and humans, as well as factors to prevent infection and transmission.

Technical Abstract: The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics, and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data, and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at http://www.fludb.org.