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Nucleic Acids Research Advance Access originally published online on October 2, 2007
Nucleic Acids Research 2008 36(Database issue):D504-D511; doi:10.1093/nar/gkm754
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Nucleic Acids Research, 2008, Vol. 36, Database issue D504-D511
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes

Yi Huang1, Susanna K. P. Lau1,2,3, Patrick C. Y. Woo1,2,3,* and Kwok-yung Yuen1,2,3

1Department of Microbiology, 2Research Centre of Infection and Immunology and 3State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong

*To whom correspondence should be addressed. Tel: 852 2855 4892; Fax: 852 2855 1241; Email: pcywoo{at}hkucc.hku.hk Correspondence may also be addressed to Kwok-yung Yuen. Tel: 852 2855 4892; Fax: 852 2855 1241; Email: hkumicro{at}hkucc.hku.hk

Received June 27, 2007. Revised August 24, 2007. Accepted September 11, 2007.

The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis.


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