Efficient pattern matching in degenerate strings with the Burrows–Wheeler transform - Normandie Université
Journal Articles Information Processing Letters Year : 2019

Efficient pattern matching in degenerate strings with the Burrows–Wheeler transform

Abstract

A degenerate or indeterminate string on an alphabet Σ is a sequence of non-empty subsets of Σ. Given a degenerate string t of length n, we present a new method based on the Burrows--Wheeler transform for searching for a degenerate pattern of length m in t running in O(mn) time on a constant size alphabet Σ. Furthermore, it is a hybrid pattern-matching technique that works on both regular and degenerate strings. A degenerate string is said to be conservative if its number of non-solid letters is upper-bounded by a fixed positive constant q; in this case we show that the search complexity time is O(qm2). Experimental results show that our method performs well in practice.

Dates and versions

hal-02113307 , version 1 (28-04-2019)

Identifiers

Cite

J.W. Daykin, Richard Groult, Y. Guesnet, T. Lecroq, A. Lefebvre, et al.. Efficient pattern matching in degenerate strings with the Burrows–Wheeler transform. Information Processing Letters, 2019, 147, pp.82-87. ⟨10.1016/j.ipl.2019.03.003⟩. ⟨hal-02113307⟩
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