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

Authors:
Raphaël Clifford;Ely Porat
Affiliations:
University of Bristol, Dept. of Computer Science, Bristol, UK;Bar-Ilan University, Dept. of Computer Science, Ramat-Gan, Israel
Venue:
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
Year:
2007

Citing 10
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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 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 O(nm1/3 k1/3 log2/3 m) time. The location of the mismatches at each alignment is also given at no extra cost.