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Maximal Repetitions and Application to DNA sequences

Mathieu Giraud 1 Gregory Kucherov 2
2 POLKA - Polynomials, Combinatorics, Arithmetic
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : In this paper we describe an implementation of Main-Kolpakov-Kucherov algorithm \cite{KolpakovKucherovFOCS99} of linear-time search for maximal repetitions in sequences. We first present a theoretical background and sketch main components of the method. We also discuss how the method can be generalized to finding approximate repetitions. Then we discuss implementation decisions and present test examples of running the programs on real DNA data.
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https://hal.inria.fr/inria-00107854
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Submitted on : Thursday, October 19, 2006 - 9:11:58 AM
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Mathieu Giraud, Gregory Kucherov. Maximal Repetitions and Application to DNA sequences. Journées Ouvertes : Biologie, Informatique et Mathématiques - JOBIM'2000, 2000, Montpellier/France, pp.165--172. ⟨inria-00107854⟩

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