A Comparison of Approximate String Matching Algorithms

Experimental comparison of the running time of approximate string matching algorithms for the k differences problem is presented. Given a pattern string, a text string, and integer k, the task is to find all approximate occurrences of the pattern in the text with at most k differences (insertions, deletions, changes). We consider seven algorithms based on different approaches including dynamic programming, Boyer-Moore string matching, suffix automata, and the distribution of characters. It turns out that none of the algorithms is the best for all values of the problem parameters, and the speed differences between the methods can be considerable.