Fast bit-vector algorithms for approximate string matching under indel distance

Authors:
Heikki Hyyrö;Yoan Pinzon;Ayumi Shinohara
Affiliations:
PRESTO, Japan Science and Technology Agency (JST), Japan;Department of Computer Science, King's College, London, UK;PRESTO, Japan Science and Technology Agency (JST), Japan
Venue:
SOFSEM'05 Proceedings of the 31st international conference on Theory and Practice of Computer Science
Year:
2005

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Abstract

The approximate string matching problem is to find all locations at which a query p of length m matches a substring of a text t of length n with at most k differences (insertions, deletions, substitutions). The fastest solutions in practice for this problem are the bit-parallel NFA simulation algorithms of Wu & Manber [4] and Baeza-Yates & Navarro [1], and the bit-parallel dynamic programming algorithm of Myers [3]. In this paper we present modified versions of these algorithms to deal with the restricted case where only insertions and deletions (called indel for short) are permitted. We also show test results with the algorithms.