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

Authors: Nadia Ben Nsira; Thierry Lecroq; Élise Prieur-Gaston

Addresses: Normandie University, UNIROUEN, LITIS, 76000 Rouen, France ' Normandie University, UNIROUEN, LITIS, 76000 Rouen, France ' Normandie University, UNIROUEN, LITIS, 76000 Rouen, France

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.

Keywords: computational biology; bioinformatics; algorithm design; pattern matching; string matching; DNA sequences; genomic sequences; Landau-Vishkin algorithm; Aho-Corasick algorithm; similar sequences.

DOI: 10.1504/IJDMB.2019.099285

International Journal of Data Mining and Bioinformatics, 2019 Vol.22 No.1, pp.1 - 18

Received: 12 Jan 2019
Accepted: 28 Jan 2019
Published online: 24 Apr 2019 *

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