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

J.W. Daykin Richard Groult 1 Y. Guesnet 2 T. Lecroq 2 A. Lefebvre 2 M. Leonard 2 L. Mouchard 2 É. Prieur-Gaston 2 B. Watson
1 MIS - Modélisation, Information et Systèmes - UR UPJV 4290
2 TIBS - LITIS - Equipe Traitement de l'information en Biologie Santé
LITIS - Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes
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.
Keywords : Algorithm Burrows–Wheeler transform Degenerate Pattern matching String
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https://hal-normandie-univ.archives-ouvertes.fr/hal-02113307
Contributor : Thierry Lecroq <>
Submitted on : Sunday, April 28, 2019 - 3:46:40 PM
Last modification on : Monday, June 7, 2021 - 12:02:01 PM

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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, Elsevier, 2019, 147, pp.82-87. ⟨10.1016/j.ipl.2019.03.003⟩. ⟨hal-02113307⟩

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