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Nucleic Acids Research, 2003, Vol. 31, No. 13 3672-3678
© 2003 Oxford University Press

mreps: efficient and flexible detection of tandem repeats in DNA

Roman Kolpakov, Ghizlane Bana1 and Gregory Kucherov*,1

French–Russian Institute for Informatics and Applied Mathematics, Moscow University, 119899 Moscow, Russia 1 INRIA-Lorraine/LORIA, 615, rue du Jardin Botanique, BP 101, 54602 Villers-lès-Nancy, France

*To whom correspondence should be addressed. Tel: +33 3 83 59 30 21; Fax: +33 3 83 27 83 19; Email: gregory.kucherov{at}loria.fr

The presence of repeated sequences is a fundamental feature of genomes. Tandemly repeated DNA appears in both eukaryotic and prokaryotic genomes, it is associated with various regulatory mechanisms and plays an important role in genomic fingerprinting. In this paper, we describe mreps, a powerful software tool for a fast identification of tandemly repeated structures in DNA sequences. mreps is able to identify all types of tandem repeats within a single run on a whole genomic sequence. It has a resolution parameter that allows the program to identify ‘fuzzy’ repeats. We introduce main algorithmic solutions behind mreps, describe its usage, give some execution time benchmarks and present several case studies to illustrate its capabilities. The mreps web interface is accessible through http://www.loria.fr/mreps/.


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