A fast Boyer-Moore type pattern matching algorithm for highly similar sequences Online publication date: Wed, 30-Sep-2015
by Nadia Ben Nsira; Thierry Lecroq; Mourad Elloumi
International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 13, No. 3, 2015
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.
Existing subscribers:
Go to Inderscience Online Journals to access the Full Text of this article.
If you are not a subscriber and you just want to read the full contents of this article, buy online access here.Complimentary Subscribers, Editors or Members of the Editorial Board of the International Journal of Data Mining and Bioinformatics (IJDMB):
Login with your Inderscience username and password:
Want to subscribe?
A subscription gives you complete access to all articles in the current issue, as well as to all articles in the previous three years (where applicable). See our Orders page to subscribe.
If you still need assistance, please email subs@inderscience.com
Our Blog 
Follow us on Twitter 
Visit us on Facebook