A Scalable Coprocessor for Bioinformatic Sequence Alignments

A hardware coprocessor for the rapid calculation of bioinformatic sequence alignments is presented. The coprocessor uses a globally-asynchronous locally-synchronous (GALS) design style which makes the coprocessor much easier to scale as CMOS feature sizes decrease. The coprocessor is intended to be implemented on a single integrated circuit along with a simple 32-bit RISC processor and memory system. The specific sequence alignment algorithm implemented is that of Smith and Waterman, but the general design strategy could be extended to other bioinformatic sequence alignment algorithms.