Efficient string-matching allowing for non-overlapping inversions

Inversions are a class of chromosomal mutations, widely regarded as one of the major mechanisms for reorganizing the genome. In this paper we present a new algorithm for the approximate string matching problem allowing for non-overlapping inversions which runs in O(nm) worst-case time and O(m2) space, for a character sequence of size n and pattern of size m. This improves upon a previous O(nm2)-time algorithm. In addition we present a variant of our algorithm with the same complexity in the worst case, but with a O(n) time complexity in the average case. This work has been supported by Istituto Nazionale di Alta Matematica "Francesco Severi".