Maximal Repetitions and Application to DNA sequences
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.
Domains
Other [cs.OH]
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