VNTRDB: a bacterial variable number tandem repeat locus database.
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/.
Chang
Chia-Hung
CH
Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan.
Chang
Yu-Chung
YC
Underwood
Anthony
A
Chiou
Chien-Shun
CS
Kao
Cheng-Yan
CY
D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D017931:DNA Primers; D030561:Databases, Nucleic Acid; D005819:Genetic Markers; D016680:Genome, Bacterial; D020407:Internet; D018598:Minisatellite Repeats; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D014584:User-Computer Interface
D017931:DNA Primers; D005819:Genetic Markers