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arXiv · 1701.04723

A Resistive CAM Processing-in-Storage Architecture for DNA Sequence Alignment

Roman Kaplan·Leonid Yavits·Ran Ginosar·Uri Weiser
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Abstract

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 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 4.7x higher throughput and at least 15x lower power dissipation.

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Roman Kaplan, Leonid Yavits, Ran Ginosar, Uri Weiser. 2017-01-17. A Resistive CAM Processing-in-Storage Architecture for DNA Sequence Alignment. https://doi.org/10.1109/mm.2017.3211121

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