VNTRDB: a bacterial variable number tandem repeat locus database
Resource
Nucleic Acids Research 35: D416-D421
Journal
Nucleic Acids Research
Pages
D416-D421
Date Issued
2007
Date
2007
Author(s)
Chang, Chia-Hung
Chang, Yu-Chung
Underwood, Anthony
Chiou, Chien-Shun
Kao, Cheng-Yan
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/. ? 2007 Oxford University Press.
SDGs
Other Subjects
access to information; article; bacterial genome; bacterial strain; gene number; genetic identification; genetic polymorphism; Mycobacterium tuberculosis; Neisseria meningitidis; nonhuman; polymerase chain reaction; polymorphic locus; priority journal; Salmonella enterica; sequence database; species difference; variable number of tandem repeat; Variable number of tandem repeat database; Yersinia pestis; Bacteria; Databases, Nucleic Acid; DNA Primers; Genetic Markers; Genome, Bacterial; Internet; Minisatellite Repeats; Polymerase Chain Reaction; Polymorphism, Genetic; User-Computer Interface; Bacteria (microorganisms)
Type
journal article
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