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  1. VNTR Locus DB
    Full Name of the Resource : Bacterial Variable Number Tandem Repeat locus database
    Resource Category : Databases -> Genomic Databases (Non-Human) -> General Genomics Databases

    Brief Description : The VNTRDB provides comprehensive information about bacterial VNTR loci in genome sequences. This database was constructed by the method, VNTR Analyzer, developed by Chang et al., (1) and the accuracy of the database content was tested by comparing it with published TR loci. Although a similar site, GPMS, has been reported by Denoeud and Vergnaud (2), what the database provides are mainly VNTRs discovered when comparing two highly-conserved strains of a single bacterial species. But in the VNTRDB, three extra functions can be obtained: 1) A visualization tool is provided to allow users to examine or realign the alignments, it may solve those problems caused by the uncertainties of locus length or copy number; 2) To enable the discovery of more putative polymorphic tandem repeats, the comparisons were made between bacterial genomes that are not necessarily from the same species or with high levels of sequence identity; 3) The identification of unique tandem repeats. Theoretically, any unique sequence can serve as DNA marker for the identification of bacteria, so a VNTR locus that is unique could be one such marker. In order to confirm the utility of these loci for identification they would need to be tested experimentally. Although VNTRDB and GPMS were constructed by different strategies and have somewhat different database contents, the two databases are likely to serve the users in a complementary fashion.
    Subject Area : Tandem Repeat


    Institute/s :
    Department of Computer Science and Information Engineering, National Taiwan University Taipei, Taiwan
    Address of Institute/s :
    Department of Computer Science and Information Engineering, National Taiwan University Taipei, Taiwan
    Country : Taiwan

    Associated Institutes :

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

    Associated Country : Taiwan; United Kingdom


    Authors/Contributors : Chia-Hung Chang; Yu-Chung Chang; Anthony Underwood; Chien-Shun Chiou; Cheng-Yan Kao
    Contact Email : cykao@csie.ntu.edu.tw
    Year : 2006