A filtering algorithm for k-mismatch with don't cares

Authors:
Raphaël Clifford;Ely Porat
Affiliations:
University of Bristol, Dept. of Computer Science, Bristol, BS8 1UB, UK;Bar-Ilan University, Dept. of Computer Science, 52900 Ramat-Gan, Israel
Venue:
Information Processing Letters
Year:
2010

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Abstract

We present a filtering based algorithm for the k-mismatch pattern matching problem with don't cares. Given a text t of length n and a pattern p of length m with don't care symbols in either p or t (but not both), and a bound k, our algorithm finds all the places that the pattern matches the text with at most k mismatches. The algorithm is deterministic and runs in @Q(nm^1^/^3k^1^/^3log^2^/^3m) time.