Title: A fast Boyer-Moore type pattern matching algorithm for highly similar sequences

Authors: Nadia Ben Nsira; Thierry Lecroq; Mourad Elloumi

Addresses: LaTICE, University of Tunis El Manar, Tunisia ' University of Rouen, France ' LaTICE, University of Tunis El Manar, Tunisia

Abstract: In the last decade, biology and medicine have undergone a fundamental change: next generation sequencing (NGS) technologies have enabled to obtain genomic sequences very quickly and at small costs compared to the traditional Sanger method. These NGS technologies have thus permitted to collect genomic sequences (genes, exomes or even full genomes) of individuals of the same species. These latter sequences are identical to more than 99%. There is thus a strong need for efficient algorithms for indexing and performing fast pattern matching in such specific sets of sequences. In this paper we propose a very efficient algorithm that solves the exact pattern matching problem in a set of highly similar DNA sequences where only the pattern can be pre-processed. This new algorithm extends variants of the Boyer-Moore exact string matching algorithm. Experimental results show that it exhibits the best performances in practice.

Keywords: computational biology; bioinformatics; algorithm design; pattern matching; string matching; DNA sequences; genomic sequences; Boyer-Moore algorithm; similar sequences; next generation sequencing; NGS.

DOI: 10.1504/IJDMB.2015.072101

International Journal of Data Mining and Bioinformatics, 2015 Vol.13 No.3, pp.266 - 288

Received: 15 Jan 2015
Accepted: 25 Jan 2015
Published online: 30 Sep 2015 *

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