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Evol Bioinform Online. 2017 Dec 17;13:1176934317746667. doi: 10.1177/1176934317746667. eCollection 2017.

Virus Database and Online Inquiry System Based on Natural Vectors.

Author information

1
Department of Mathematical Sciences, Tsinghua University, Beijing, China.
2
Department of Mathematics, Statistics, and Computer Science, The University of Illinois at Chicago, Chicago, IL, USA.
3
Information Technology Services Center, The Hong Kong University of Science and Technology, Kowloon, Hong Kong.
4
College of Computer and Control Engineering, Nankai University, Tianjin, China.
5
Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.
6
School of Medicine, Flinders University, Adelaide, SA, Australia.
7
Department of Biological Sciences, Chicago State University, Chicago, IL, USA.

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.

KEYWORDS:

classification; database; genome sequences; natural vector; virus

Conflict of interest statement

Declaration of conflicting interests:The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

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