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mreps: efficient and flexible detection of tandem repeats in DNA

Roman Kolpakov Ghizlane Bana 1 Gregory Kucherov 1
1 ADAGE - Applying discrete algorithms to genomics
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : 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 capable to identify all types of tandem repeats within a single program run; 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 {\tt http://www.loria.fr/mreps/}.
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https://hal.inria.fr/inria-00099597
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Submitted on : Tuesday, September 26, 2006 - 9:39:07 AM
Last modification on : Friday, February 26, 2021 - 3:28:02 PM

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  • HAL Id : inria-00099597, version 1

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Roman Kolpakov, Ghizlane Bana, Gregory Kucherov. mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Research, Oxford University Press, 2003, 31 (13), pp.3672-3678. ⟨inria-00099597⟩

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