A Survey of FPGAs for Acceleration of High Performance Computing and their Application to Computational Molecular Biology

Molecular biocomputation workflows traditionally involve days of compute time to align DNA/protein sequences. Custom computing machines (CCMs) provide a means to dramatically reduce alignment time, and FPGAs provide a practical means to implement such CCMs. Software implementation of some sequence alignment algorithms suffer quadratic time performance, however CCM implementations may be highly parallelized and consequently provide linear time performance. Similarly, CCMs may be used to accelerate workflows or operations in a wide range of domains, often dramatically outperforming large scale clusters. Programming and integration problems limit CCM usage, though progress has been made to overcome these problems. With continued development of tools, devices, and integration solutions, CCMs on FPGAs coupled to conventional systems present an effective architecture for high performance computing.