We study the classical approximate string matching problem, that is, given
strings P and Q and an error threshold k, find all ending positions of
substrings of Q whose edit distance to P is at most k. Let P and Q
have lengths m and n, respectively. On a standard unit-cost word RAM with
word size w≥logn we present an algorithm using time O(nk⋅min(lognlog2m,wlog2mlogw)+n) When P is
short, namely, m=2o(logn) or m=2o(w/logw) this
improves the previously best known time bounds for the problem. The result is
achieved using a novel implementation of the Landau-Vishkin algorithm based on
tabulation and word-level parallelism.Comment: To appear in Theory of Computing System