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

TL;DR

This paper proposes a novel resistive CAM-based processing-in-storage architecture for DNA sequence alignment, achieving significantly higher throughput and lower power consumption compared to traditional FPGA, Xeon Phi, and GPU solutions.

Contribution

It introduces a new ReCAM-based architecture and algorithm for DNA sequence alignment that outperforms existing hardware implementations in speed and power efficiency.

Findings

At least 4.7x higher throughput than FPGA, Xeon Phi, and GPU.

At least 15x lower power dissipation.

Massively-parallel compare operation for fixed cycle matching.

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.