Performance versus power analysis for bioinformatics sequence alignment

Due to the utilization of abundant hardware resources, power consumption is becoming an important constraint for bioinformatics sequence alignment applications. In this paper, the dynamic power consumption for such applications and its impact on performance is evaluated. Additionally, resource utilization and performance results are provided for implementation with a number of different FPGA platforms. The results obtained using Xilinx ISE tools and Matlab demonstrate that the performance per unit Watt increases rapidly when increasing the number of Processing Elements (PEs). Increasing the number of PEs beyond a certain number slows down the performance per unit Watt significantly. This behavior is used for approximating the number of PEs that gives an optimized performance per unit Watt.