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. 2003 Jul 1;31(13):3672-8.
doi: 10.1093/nar/gkg617.

mreps: Efficient and flexible detection of tandem repeats in DNA

Roman Kolpakov  1 , Ghizlane Bana, Gregory Kucherov
Affiliations

mreps: Efficient and flexible detection of tandem repeats in DNA

Roman Kolpakov et al. Nucleic Acids Res. .

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 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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Figures

Figure 1
Figure 1
Flowchart of the algorithm.
Figure 2
Figure 2
Threshold error rate for filtering our statistically expected repeats (quality filter). Typical simulation results, together with the threshold error rate, are shown for values 1, 3, 10, 20 of the resolution parameter. Each picture shows the threshold error rate function and the error rate of repeats found in a pseudo-random DNA sequence. The three thickness levels of points distinguish the number of found repeats with the same length and error rate (see the legend).
Figure 3
Figure 3
Excerpts of mreps output. (A) Resolution 5 and (B) resolution 18.
Figure 3
Figure 3
Excerpts of mreps output. (A) Resolution 5 and (B) resolution 18.
See this image and copyright information in PMC

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