FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology

Lars Rønn Olsen, Guang Lan Zhang, Ellis L. Reinherz, Vladimir Brusic

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    Abstract

    Background: The flavivirus genus is unusually large, comprising more than 70 species, of which more than half are known human pathogens. It includes a set of clinically relevant infectious agents such as dengue, West Nile, yellow fever, and Japanese encephalitis viruses. Although these pathogens have been studied extensively, safe and efficient vaccines lack for the majority of the flaviviruses. 

    Results: We have assembled a database that combines antigenic data of flaviviruses, specialized analysis tools, and workflows for automated complex analyses focusing on applications in immunology and vaccinology. FLAVIdB contains 12,858 entries of flavivirus antigen sequences, 184 verified T-cell epitopes, 201 verified B-cell epitopes, and 4 representative molecular structures of the dengue virus envelope protein. FLAVIdB was assembled by collection, annotation, and integration of data from GenBank, GenPept, UniProt, IEDB, and PDB. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). Further annotation of selected functionally relevant features was performed by organizing information extracted from the literature. The database was incorporated into a web-accessible data mining system, combining specialized data analysis tools for integrated analysis of relevant data categories (protein sequences, macromolecular structures, and immune epitopes). The data mining system includes tools for variability and conservation analysis, T-cell epitope prediction, and characterization of neutralizing components of B-cell epitopes. FLAVIdB is accessible at cvc.dfci.harvard.edu/flavi/ 

    Conclusion: FLAVIdB represents a new generation of databases in which data and tools are integrated into a data mining infrastructures specifically designed to aid rational vaccine design by discovery of vaccine targets.
    Original languageEnglish
    JournalImmunome Research
    Volume7
    Issue number3
    Number of pages9
    ISSN1745-7580
    Publication statusPublished - 2011

    Bibliographical note

    This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

    Keywords

    • Immunology
    • Molecular Biology
    • Computational Theory and Mathematics
    • Applied Mathematics
    • Computer Science Applications
    • virus envelope protein
    • antigenicity
    • automation
    • B lymphocyte
    • conference paper
    • data base
    • data mining
    • Dengue virus
    • Flavivirus
    • molecular dynamics
    • nonhuman
    • structure analysis
    • T lymphocyte
    • vaccination
    • Japanese encephalitis virus group

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