Abstract
Conference Title: 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Conference Start Date: 2014, Nov. 2 Conference End Date: 2014, Nov. 5 Conference Location: Belfast, United Kingdom With the advent of NGS technologies there are more and more genomic sequences of individuals of the same species available. These sequences only differ by a very small amount. 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 a very efficient algorithm that solves the on-line exact pattern matching problem in a set of highly similar DNA sequences. The algorithm we propose extends variants of the Boyer-Moore exact string matching algorithm. Experimental results show that our new algorithm exhibits the best performances in practice.