Efficient computation of the Damerau-Levenshtein distance between biological sequences

Abstract

We have developed linear space algorithms to compute the Damerau-Levenshtein (DL) distance [1], [2] between two strings and also to find a sequence of edit operations of length equal to the DL distance (optimal trace). Our algorithms require O(s min{m, n} + m + n) space, where s is the size of the alphabet and m and n are, respectively, the lengths of the two strings. Previously known algorithms require O(mn) space. Cache efficient and multi-core linear-space algorithms have also been developed. The cache miss efficiency of the algorithms was analyzed using a simple cache model.