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Related Experiment Videos

VNTRDB: a bacterial variable number tandem repeat locus database.

Chia-Hung Chang1, Yu-Chung Chang, Anthony Underwood

  • 1Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan.

Nucleic Acids Research
|December 19, 2006
PubMed
Summary
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A new database (VNTRDB) aids in discovering variable number tandem repeats (TRs) for microbial molecular typing. This resource facilitates epidemiological surveillance by providing flanking sequences for PCR primer design.

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Variable number tandem repeat-PCR (VNTR-PCR) is crucial for microbial molecular typing and epidemiological studies.
  • Limited availability of identified TRs from genomic data hinders bacterial surveillance.
  • Comparative genome analysis is essential for discovering novel TR loci.

Purpose of the Study:

  • To introduce a freely accessible database (VNTRDB) for identifying polymorphic tandem repeat loci.
  • To support assay design for PCR primer development in molecular epidemiology.
  • To enhance bacterial surveillance through improved molecular typing tools.

Main Methods:

  • Comparative genome analysis to identify putatively polymorphic tandem repeat loci.
  • TR locus discovery by comparing sequences across bacterial genera, species, and strains.

Related Experiment Videos

  • Development of a visualization tool for assessing copy number and locus length accuracy.

    • Main Results:

    • The VNTRDB provides flanking sequences for PCR primer design.
    • TRs unique to specific bacterial genera can be identified.
    • The database aids in discovering polymorphic TR loci for molecular epidemiology.

    Conclusions:

    • The VNTRDB is a valuable resource for microbial molecular typing and epidemiological surveillance.
    • Facilitates the discovery and application of VNTR markers in bacterial research.
    • Enhances the utility of VNTR-PCR for tracking microbial populations.