Abstract
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/.
| Original language | English |
|---|---|
| Pages (from-to) | D416-D421 |
| Journal | Nucleic Acids Research |
| Volume | 35 |
| Issue number | SUPPL. 1 |
| DOIs | |
| Publication status | Published - Jan 2007 |
Bibliographical note
Funding Information: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. The authors also want to thank NCBI, TIGR and Sanger Institute for provide bacterial sequences for VNTR analysis. Funding to pay the Open Access publication charges for this article was provided by Institute for Information Industry (III), Taiwan.