Hardware acceleration of sequence alignment algorithms-an overview

Sequence alignment is one of the most important activities in bioinformatics. With the ever increasing volume of data in bioinformatics databases, the time for comparing a query sequence with the available databases is always increasing. Many algorithms have been proposed to perform and accelerate sequence alignment activities. This paper introduces a taxonomy of the various sequence alignment algorithms found in the literature, with particular emphasis on the Smith-Waterman (S-W) algorithm. The paper also provides a classification of the available hardware acceleration methods used to speed up the S-W algorithm.