Biological sequence alignment is an essential tool used in molecular biology and biomedical applications.The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner.Known Ball - Batter - Mask methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks.A space-efficient, global sequence alignment algorithm and ONE PIECE architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations.With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000.
For greater performance, the architecture is scalable to more processing elements.