A novel processing-in-storage (PRinS) architecture based on Resistive CAM (ReCAM) is described and proposed for Smith-Waterman (S-W) sequence alignment. The ReCAM PRinS massively parallel compare operation finds matching base pairs in a fixed number of cycles, regardless of sequence length. The ReCAM PRinS S-W algorithm is simulated and compared to FPGA, Xeon Phi, and GPU-based implementations, showing at least 4.7 times higher throughput and at least 15 times lower power dissipation.
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Kaplan et al. (2017) studied this question.
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