Using graphics hardware to accelerate biological sequence database scanning

Sequence alignment is a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the rapid growth rate of biological sequence databases. In this paper we present a new approach to high performance biological sequence database scanning on graphics processing units. Using modern graphics processing units for high performance computing is facilitated by their enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have reformulated the Smith-Waterman dynamic programming algorithm in terms of computer graphics primitives. This results in an implementation with significant runtime savings on two standard off-the-shelf computer graphics cards. To our knowledge this is the first reported mapping of biological sequence alignment onto a graphics processing unit.