Database
MyBASE: a database for genome polymorphism and gene function studies of Mycobacterium
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* Corresponding authors: Baoli Zhu bzhu@chori.org - Jing Wang wangjing@psych.ac.cn
- † Equal contributors
1 James D Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310007, PR China
2 Behavioral Genetics Center, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, PR China
3 Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
4 Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
5 Institute of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310029, PR China
6 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
BMC Microbiology 2009, 9:40 doi:10.1186/1471-2180-9-40
Published: 20 February 2009Abstract
Background
Mycobacterial pathogens are a major threat to humans. With the increasing availability of functional genomic data, research on mycobacterial pathogenesis and subsequent control strategies will be greatly accelerated. It has been suggested that genome polymorphisms, namely large sequence polymorphisms, can influence the pathogenicity of different mycobacterial strains. However, there is currently no database dedicated to mycobacterial genome polymorphisms with functional interpretations.
Description
We have developed a mycobacterial database (MyBASE) housing genome polymorphism data and gene functions to provide the mycobacterial research community with a useful information resource and analysis platform. Whole genome comparison data produced by our lab and the novel genome polymorphisms identified were deposited into MyBASE. Extensive literature review of genome polymorphism data, mainly large sequence polymorphisms (LSPs), operon predictions and curated annotations of virulence and essentiality of mycobacterial genes are unique features of MyBASE. Large-scale genomic data integration from public resources makes MyBASE a comprehensive data warehouse useful for current research. All data is cross-linked and can be graphically viewed via a toolbox in MyBASE.
Conclusion
As an integrated platform focused on the collection of experimental data from our own lab and published literature, MyBASE will facilitate analysis of genome structure and polymorphisms, which will provide insight into genome evolution. Importantly, the database will also facilitate the comparison of virulence factors among various mycobacterial strains. MyBASE is freely accessible via http://mybase.psych.ac.cn webcite.