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

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.

References in corpus (1)

• SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors

Cited by in corpus (8)

• pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables
• Hamming Distance Tolerant Content-Addressable Memory (HD-CAM) for Approximate Matching Applications
• ASAP: Accelerated Short-Read Alignment on Programmable Hardware
• RAPIDx: High-performance ReRAM Processing in-Memory Accelerator for Sequence Alignment
• BioSEAL: In-Memory Biological Sequence Alignment Accelerator for Large-Scale Genomic Data
• Read Mapping Near Non-Volatile Memory
• FindeR: Accelerating FM-Index-based Exact Pattern Matching in Genomic Sequences through ReRAM technology
• EXMA: A Genomics Accelerator for Exact-Matching