PERFORMANCE EVALUATION FOR RVE-BASED FPGA ACCELERATION OF GENETIC SEQUENCE ALIGNMENT

L. HASAN, H. ZAFAR

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.


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