## What is mreps

mreps is a flexible and efficient
software for identifying serial repeats (usually called *tandem
repeats*) in DNA sequences. It was developed in the years 2000-2005 at
LORIA in former Adage group and
is currently maintained by Gregory Kucherov.

See a mini-tutorial of mreps for more explanations on what mreps computes.

The following paper describes mreps together with some examples of its application. Please cite this paper when referring to mreps.

**[1]** R. Kolpakov, G. Bana, and G. Kucherov, mreps: efficient and flexible detection of tandem repeats in DNA, **Nucleic Acid Research**, 31 (13), July 1 2003, pp 3672-3678.

Combinatorial algorithms implemented in mreps have been presented in the following publications.

**[2]** R. Kolpakov, G. Kucherov, Finding maximal repetitions in a word in linear time, **1999 Symposium on Foundations of Computer Science (FOCS)**, New-York (USA), pp. 596-604, IEEE Computer Society

**[3]** R. Kolpakov, G. Kucherov, Finding
approximate repetitions under Hamming distance,
**Theoretical Computer Science**, 2003, vol 303 (1), pp
135-156. An extended abstract appeared in* the 9th European
Symposium on Algorithms* (ESA 2001), Aarhus, Denmark, 2001

## Download, install and use it!

Go to the Help page, all instructions are there## Run it via a Web interface

You can run mreps via a Web interface (on an external server). Try it!## Some features of mreps

**Mixed combinatorial/heuristic approach**

mreps is based on a mixed combinatorial/heuristic paradigm. The core of mreps is constituted by exhaustive combinatorial algorithms (described in [2,3]) used to find **all**
repeats verifying certain mathematical properties. This insures the
exhaustivity of the approach. Those repeats are then submitted to an
heuristic treatment in order to obtain more biologically relevant
representation of the repeats. A description of mreps can be found in [1].

**Identifying "fuzzy" repeats**

mreps has a resolution parameter that allows to compute

*"fuzzy"*repeats. In metaphoric terms, this parameter plays the role of

*"magnifying glass"*allowing to

*"zoom out"*the genomic sequence in order to compute looser repeats.

**Efficiency**

mreps has no limitation whatsoever on the pattern size (size of
the repeated unit) of computed repeats -- repeats of all possible
pattern sizes can be computed within a single program run. Moreover,
depending on the resolution parameter, this run is very fast: for low
resolution values processing sequences of dozens of millions bases takes
only several seconds on a regular PC.

**Limitations**

mreps algorithm does not deal with indels (insertions/deletions
of nucleotides), but only with substitutions. As a result, indels are
treated in an indirect way, and certain repeats containing indels may be
missed.

## Credits

The following people contributed to mreps: Ghizlane Bana, Mathieu Giraud, Liliana Ibanescu, Roman Kolpakov, Gregory Kucherov, Ralph Rabbat

For questions about mreps or for bug reports, please contact