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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...

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Autores principales: Chang, Chia-Hung, Chang, Yu-Chung, Underwood, Anthony, Chiou, Chien-Shun, Kao, Cheng-Yan
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781188/
https://www.ncbi.nlm.nih.gov/pubmed/17175529
http://dx.doi.org/10.1093/nar/gkl872
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author Chang, Chia-Hung
Chang, Yu-Chung
Underwood, Anthony
Chiou, Chien-Shun
Kao, Cheng-Yan
author_facet Chang, Chia-Hung
Chang, Yu-Chung
Underwood, Anthony
Chiou, Chien-Shun
Kao, Cheng-Yan
author_sort Chang, Chia-Hung
collection PubMed
description 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 .
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spelling pubmed-17811882007-02-22 VNTRDB: a bacterial variable number tandem repeat locus database Chang, Chia-Hung Chang, Yu-Chung Underwood, Anthony Chiou, Chien-Shun Kao, Cheng-Yan Nucleic Acids Res Articles 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 . Oxford University Press 2007-01 2006-12-14 /pmc/articles/PMC1781188/ /pubmed/17175529 http://dx.doi.org/10.1093/nar/gkl872 Text en © 2006 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Chang, Chia-Hung
Chang, Yu-Chung
Underwood, Anthony
Chiou, Chien-Shun
Kao, Cheng-Yan
VNTRDB: a bacterial variable number tandem repeat locus database
title VNTRDB: a bacterial variable number tandem repeat locus database
title_full VNTRDB: a bacterial variable number tandem repeat locus database
title_fullStr VNTRDB: a bacterial variable number tandem repeat locus database
title_full_unstemmed VNTRDB: a bacterial variable number tandem repeat locus database
title_short VNTRDB: a bacterial variable number tandem repeat locus database
title_sort vntrdb: a bacterial variable number tandem repeat locus database
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781188/
https://www.ncbi.nlm.nih.gov/pubmed/17175529
http://dx.doi.org/10.1093/nar/gkl872
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