RC-BLASTn: Implementation and Evaluation of the BLASTn Scan Function

BLASTn is a tool universally used by biologists to identify similarities between nucleotide based biological genome sequences. This report describes an hardware implementation designed to accelerate algorithm maintaining the same results yielded by the software developed at NCBI. A detailed profile study identifies the Blast_Nt_Scan function as the computationally intensive part of the algorithm. A hardware component has been designed and implemented for this critical section. Rather then trying to implement more of the computation on the FPGA chip, our focus is on improving workload performance. Hence, the hardware has been designed to be replicated and placed on the FPGA to reduce initial comparison latencies between multiple short sequences(queries) and a subject database. Tests reveal the current implementation achieves an approximate 4X speedup over the software run on a modern general purpose computer generating identical results.