Finding the position of the k-mismatch and approximate tandem repeats

Authors:
Haim Kaplan;Ely Porat;Nira Shafrir
Affiliations:
School of Computer Science, Tel Aviv University, Tel Aviv, Israel;Department of Mathematics and Computer Science, Bar-Ilan University, Ramat-Gan, Israel;School of Computer Science, Tel Aviv University, Tel Aviv, Israel
Venue:
SWAT'06 Proceedings of the 10th Scandinavian conference on Algorithm Theory
Year:
2006

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Abstract

Given a pattern P, a text T, and an integer k, we want to find for every position j of T, the index of the k-mismatch of P with the suffix of T starting at position j. We give an algorithm that finds the exact index for each j, and algorithms that approximate it. We use these algorithms to get an efficient solution for an approximate version of the tandem repeats problem with k-mismatches