On string matching with k mismatches

Abstract

In this paper we consider several variants of the pattern matching problem. In particular, we investigate the following problems: 1) Pattern matching with k mismatches; 2) Approximate counting of mismatches; and 3) Pattern matching with mismatches. The distance metric used is the Hamming distance. We present some novel algorithms and techniques for solving these problems. Both deterministic and randomized algorithms are offered. Variants of these problems where there could be wild cards in either the text or the pattern or both are considered. An experimental evaluation of these algorithms is also presented. The source code is available at http://www.engr.uconn.edu/~man09004/kmis.zip.