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

Jacqueline W. Daykin, Richard Groult, Yannick Guesnet, Thierry Lecroq, Arnaud Lefebvre, Martine Léonard, Laurent Mouchard, Élise Prieur-Gaston, Bruce Watson

Allbwn ymchwil: Papur gweithio


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
Iaith wreiddiolSaesneg
StatwsCyhoeddwyd - 03 Awst 2017

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Gweld gwybodaeth am bynciau ymchwil 'Efficient pattern matching in degenerate strings with the Burrows-Wheeler transform'. Gyda’i gilydd, maen nhw’n ffurfio ôl bys unigryw.

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