An innovative reconfigurable supercomputing platform—XD1000—is being developed by XtremeData to exploit the rapid progress of FPGA technology and the high performance of HyperTransport interconnection. In this paper, we present implementations of the Smith-Waterman algorithm for both DNA and protein sequences on the platform. The
main features include: a multistage processing element (PE) design which significantly reduces the FPGA resource usage and allows more parallelism to be exploited; a pipelined control mechanism with uneven stage latencies—a key to minimize the overall PE pipeline cycle time; and a compressed substitution matrix storage structure, resulting in substantial decrease of the on-chip SRAM usage.