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 then- 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.