Denoeud France, Vergnaud Gilles
Laboratoire GPMS, Institut de Génétique et Microbiologie, Bat 400, Université Paris-Sud, 91405 Orsay cedex, France.
BMC Bioinformatics. 2004 Jan 12;5:4. doi: 10.1186/1471-2105-5-4.
Polymorphic tandem repeat typing is a new generic technology which has been proved to be very efficient for bacterial pathogens such as B. anthracis, M. tuberculosis, P. aeruginosa, L. pneumophila, Y. pestis. The previously developed tandem repeats database takes advantage of the release of genome sequence data for a growing number of bacteria to facilitate the identification of tandem repeats. The development of an assay then requires the evaluation of tandem repeat polymorphism on well-selected sets of isolates. In the case of major human pathogens, such as S. aureus, more than one strain is being sequenced, so that tandem repeats most likely to be polymorphic can now be selected in silico based on genome sequence comparison.
In addition to the previously described general Tandem Repeats Database, we have developed a tool to automatically identify tandem repeats of a different length in the genome sequence of two (or more) closely related bacterial strains. Genome comparisons are pre-computed. The results of the comparisons are parsed in a database, which can be conveniently queried over the internet according to criteria of practical value, including repeat unit length, predicted size difference, etc. Comparisons are available for 16 bacterial species, and the orthopox viruses, including the variola virus and three of its close neighbors.
We are presenting an internet-based resource to help develop and perform tandem repeats based bacterial strain typing. The tools accessible at http://minisatellites.u-psud.fr now comprise four parts. The Tandem Repeats Database enables the identification of tandem repeats across entire genomes. The Strain Comparison Page identifies tandem repeats differing between different genome sequences from the same species. The "Blast in the Tandem Repeats Database" facilitates the search for a known tandem repeat and the prediction of amplification product sizes. The "Bacterial Genotyping Page" is a service for strain identification at the subspecies level.
多态串联重复序列分型是一项新的通用技术，已被证明对炭疽芽孢杆菌、结核分枝杆菌、铜绿假单胞菌、嗜肺军团菌、鼠疫耶尔森菌等细菌病原体非常有效。先前开发的串联重复序列数据库利用越来越多细菌的基因组序列数据发布来促进串联重复序列的识别。然后，检测方法的开发需要在精心挑选的分离株集合上评估串联重复序列多态性。对于主要的人类病原体，如金黄色葡萄球菌，正在对不止一个菌株进行测序，因此现在可以基于基因组序列比较在计算机上选择最可能具有多态性的串联重复序列。
除了先前描述的通用串联重复序列数据库外，我们还开发了一种工具，用于自动识别两个（或更多）密切相关细菌菌株的基因组序列中不同长度的串联重复序列。基因组比较是预先计算的。比较结果被解析到一个数据库中，可以根据包括重复单元长度、预测大小差异等实际价值标准通过互联网方便地查询。可获得16种细菌物种以及正痘病毒（包括天花病毒及其三个近亲）的比较结果。
我们正在提供一个基于互联网的资源，以帮助开发和进行基于串联重复序列的细菌菌株分型。可在http://minisatellites.u-psud.fr访问的工具现在包括四个部分。串联重复序列数据库可识别整个基因组中的串联重复序列。菌株比较页面可识别同一物种不同基因组序列之间不同的串联重复序列。“在串联重复序列数据库中进行Blast”有助于搜索已知的串联重复序列并预测扩增产物大小。“细菌基因分型页面”是一项用于亚种水平菌株鉴定的服务。
