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VNTR Locus Database


NAR Molecular Biology Database Collection entry number 965
Chang C.H.1,2, Chang Y.C.3, Underwood A.4, Chiou C.S.5, Kao C.Y.1
1Department of Computer Science and Information Engineering, 2Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
3Department of Biotechnology, Ming Chuan University, Taoyuan, Taiwan
4Bioinformatics Unit Central Public Health Laboratory Health Protection Agency, London, UK
5Center for Disease Control, Taiwan

Database Description

The VNTRDB provides comprehensive information about bacterial VNTR loci in genome sequences. This database was constructed by the method, VNTR Analyzer, developed by Chang et al., (1) and the accuracy of the database content was tested by comparing it with published TR loci. Although a similar site, GPMS, has been reported by Denoeud and Vergnaud (2), what the database provides are mainly VNTRs discovered when comparing two highly-conserved strains of a single bacterial species. But in the VNTRDB, three extra functions can be obtained: 1) A visualization tool is provided to allow users to examine or realign the alignments, it may solve those problems caused by the uncertainties of locus length or copy number; 2) To enable the discovery of more putative polymorphic tandem repeats, the comparisons were made between bacterial genomes that are not necessarily from the same species or with high levels of sequence identity; 3) The identification of unique tandem repeats. Theoretically, any unique sequence can serve as DNA marker for the identification of bacteria, so a VNTR locus that is unique could be one such marker. In order to confirm the utility of these loci for identification they would need to be tested experimentally. Although VNTRDB and GPMS were constructed by different strategies and have somewhat different database contents, the two databases are likely to serve the users in a complementary fashion.

Acknowledgements

This work was partially supported by grants NSC93-3112-B-002-022 and NSC92-2313-B-130-001 from the National Science Council, and grant COA95-13.3.2-BAPHIQ-B1 from Bureau of Animal and Plant Health Inspection and Quarantine.

References

1. Chang, C.H., Chuang, H. Y., Chiang, Y. H., Chiou, C. S., Lu, H. I., and Kao, C. Y. (2004) Automatically predicting possible loci of variable number of tandem repeats. BIBE’04,
2. Denoeud, F. and Vergnaud, G. (2004) Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains: a Web-based resource. BMC Bioinformatics, 5, 4.


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