Performance Evaluation for RVE-based FPGA Acceleration of Genetic Sequence Alignment

Abstract

In this paper, Recursive Variable Expansion (RVE)-based Field-Programmable Gate Array (FPGA) acceleration of genetic sequence alignment and its comparison with traditional systolic array based acceleration is presented. The paper evaluates performance of the RVE-based FPGA acceleration for various blocking factors using performance metrics like throughput and throughput per area. The result is a better understanding of the RVE implications as the previous papers on the subject only considers latency as a performance metric.