Circular pattern matching with k mismatches
Presented at the International Symposium on Fundamentals of Computation Theory (August 2019), Copenhagen, Denmark
The k-mismatch problem consists in computing the Hamming distance between a pattern P of length m and every length-m substring of a text T of length n, if this distance is no more than k. In many real-world applications, any cyclic shift of P is a relevant pattern, and thus one is interested in computing the minimal distance of every length-m substring of T and any cyclic shift of P. This is the circular pattern matching with k mismatches (k-CPM) problem. A multitude of papers have been devoted to solving this problem but, to the best of our knowledge, only average-case upper bounds are known. In this paper, we present the first non-trivial worst-case upper bounds for the k-CPM problem. Specifically, we show an O(nk)-time algorithm and an -time algorithm. The latter algorithm applies in an extended way a technique that was very recently developed for the k-mismatch problem [Bringmann et al., SODA 2019].
|Lecture Notes in Computer Science/Lecture Notes in Artificial Intelligence|
|International Symposium on Fundamentals of Computation Theory|
|Organisation||Centrum Wiskunde & Informatica, Amsterdam (CWI), The Netherlands|
Charalampopoulos, P, Kociumaka, T, Pissis, S, Radoszewski, J, Rytter, W, Straszyński, J, … Zuba, W.P. (2019). Circular pattern matching with k mismatches. In Proceedings of Fundamentals of Computation Theory (pp. 213–228). doi:10.1007/978-3-030-25027-0_15