Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-ba

Background: 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. Results: 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. Geno...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: France Denoeud, Gilles Vergnaud
• Keywords: BMCBI 2004, Tandem, Tandem Repeat, Tandem Repeats Database