ESL based Smith-Waterman engine

Abstract

Sequence alignment is a key operation in computional biology. To determine similar regions between two nucleotide or protein sequences, the Smith-Waterman (SW) algorithm is a widely used algorithm to compare segments of all possible lengths and optimizes the similarity measure. As the sequence database keeps growing significantly, the deditated hardware is needd to facilitate faster SW operation. In design methodology aspect, Electronic System Level (ESL) has emerged as a practical to the rapid implementation of specific algorithm. In this paper, an ESL based development is adopted and the design space for SW implementation is explored using ESL method. The experiments show the performance of SW calculation can be speed up as 2.5 times with roughly 1.6 more gate count. Also, the development cycle is shortened significantly. Therefore, the benefit of ESL method is demonstrated. © Springer-Verlag 2012.