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

7 Citations (Scopus)

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
JournalEvolutionary Bioinformatics
Volume13
DOIs
Publication statusPublished or Issued - 15 Dec 2017

Keywords

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

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Computer Science Applications

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