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

Roman Kaplan; Leonid Yavits; Ran Ginosar; Uri Weiser

doi:10.1109/MM.2017.3211121

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

Roman Kaplan, Leonid Yavits, Ran Ginosar, Uri Weiser

Research output: Contribution to journal › Article › peer-review

55 Scopus citations

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 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.

Original language	English
Article number	8013498
Pages (from-to)	20-28
Number of pages	9
Journal	IEEE Micro
Volume	37
Issue number	4
DOIs	https://doi.org/10.1109/MM.2017.3211121
State	Published - 2017
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2017 IEEE.

Funding

This work was partially funded by the Intel Collaborative Research Institute for Computational Intelligence.

Funders	Funder number
Intel Collaboration Research Institute for Computational Intelligence

Keywords

local sequence alignment
near data computing
processing in storage
resistive RAM

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10.1109/MM.2017.3211121

Cite this

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

Abstract

Bibliographical note

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Keywords

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