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Fast practical online exact single and multiple pattern matching algorithms in highly similar sequences

Nadia Ben Nsira 1 Thierry Lecroq 1 Élise Prieur Gaston 1
1 TIBS - LITIS - Equipe Traitement de l'information en Biologie Santé
LITIS - Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes
Abstract : With the advent of high-throughput sequencing technologies there are more and more genomic sequences of individuals of the same species available. These sequences only differ by a very small amount of variations. There is thus a strong need for efficient algorithms for performing fast pattern matching in such specific sets of sequences. In this paper, we propose efficient practical algorithms that solve on-line exact pattern matching problem in a set of highly similar DNA sequences. We first present a method for exact single pattern matching when k variations are allowed in a window which size is equal to the pattern length. We then propose an algorithm for exact multiple pattern matching when only one variation is allowed in a window which size is equal to the length of the longest pattern. Experimental results show that our algorithms, though not optimal in the worst case, have good performances in practice.
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https://hal-normandie-univ.archives-ouvertes.fr/hal-02113316
Contributor : Thierry Lecroq <>
Submitted on : Sunday, April 28, 2019 - 3:57:33 PM
Last modification on : Thursday, June 27, 2019 - 6:48:47 PM

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Nadia Ben Nsira, Thierry Lecroq, Élise Prieur Gaston. Fast practical online exact single and multiple pattern matching algorithms in highly similar sequences. International Journal of Data Mining and Bioinformatics, Inderscience, 2019, 22 (1), pp.1. ⟨10.1504/IJDMB.2019.099285⟩. ⟨hal-02113316⟩

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