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Nucleic Acids Research Advance Access originally published online on December 14, 2006
Nucleic Acids Research 2007 35(Database issue):D416-D421; doi:10.1093/nar/gkl872
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Nucleic Acids Research, 2007, Vol. 35, Database issue D416-D421
© 2006 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

VNTRDB: a bacterial variable number tandem repeat locus database

Chia-Hung Chang1,2, Yu-Chung Chang3, Anthony Underwood4, Chien-Shun Chiou5 and Cheng-Yan Kao1,6,*

1 Department of Computer Science and Information Engineering, National Taiwan University Taipei, Taiwan 2 Department of Electrical Engineering, National Taiwan University Taipei, Taiwan 3 Department of Biotechnology, Ming Chuan University Taoyuan, Taiwan 4 Bioinformatics Unit Central Public Health Laboratory Health Protection Agency London, UK 5 Center for Disease Control Taiwan 6 Institute for Information Industry Taiwan

*To whom correspondence should be addressed. Tel: +886 2 23635336, ext.401; Fax: +886 2 23658741; Email: cykao{at}csie.ntu.edu.tw

Received August 10, 2006. Revised October 5, 2006. Accepted October 5, 2006.

Variable number tandem repeat-PCR (VNTR-PCR) is a novel method developed for molecular typing of microorganisms. This method has proven useful in epidemiological studies in medical microbiology. Although hundreds of bacterial genomes have been sequenced, variable number tandem repeats (TRs) derived from comparative genome analyses are scarce. This may hamper their application to the surveillance of bacteria in molecular epidemiology. Here, we present a freely accessible variable number tandem repeat database (VNTRDB) that is intended to be a resource for helping in the discovery of putatively polymorphic tandem repeat loci and to aid with assay design by providing the flanking sequences that can be used in subsequent PCR primer design. In order to reveal possible polymorphism, each TR locus was obtained by comparing the sequences between different sets of bacterial genera, species or strains. Through this comparison, TRs which are unique to a genus can also be identified. Moreover, a visualization tool is provided to ensure that the copy number and locus length of repeats are correct. The VNTRDB is available at http://vntr.csie.ntu.edu.tw/.


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