High Performance Biosequence Database Scanning using FPGAs

This paper presents the design and implementation of a generic and highly parameterised FPGA-based core for pairwise biological sequence alignment. The core is captured in the Handel-C language, which allows for high level software-like descriptions of hardware architectures. It implements the sequence alignment algorithm in hand using a pipeline of basic processing elements. This results in high performance FPGA implementations tailored to the algorithm in hand. For instance, actual hardware implementations of the Smith-Waterman algorithm for protein sequence alignment achieve speed-ups in excess of 100:1 compared to equivalent standard PC-based software implementations.