Virus Database and Online Inquiry System Based on Natural Vectors

Rui Dong, Hui Zheng, Kun Tian, Shek Chung Yau, Weiguang Mao, Wenping Yu, Changchuan Yin, Chenglong Yu, Rong Lucy He, Jie Yang, Stephen S.T. Yau

    Research output: Contribution to journalArticlepeer-review

    11 Citations (Scopus)
    50 Downloads (Pure)

    Abstract

    We construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research.

    Original languageEnglish
    Pages (from-to)1-7
    Number of pages7
    JournalEvolutionary Bioinformatics
    Volume13
    DOIs
    Publication statusPublished - 15 Dec 2017

    Bibliographical note

    Creative Commons Non Commercial CC BY-NC: This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage)

    Keywords

    • classification
    • database
    • genome sequences
    • natural vector
    • virus

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