ISMatch: A real-time hardware accelerator for inexact string matching of DNA sequences on FPGA

被引：2

作者：

Marchisio, Alberto ^{[1
]}

Teodonio, Federico ^{[2
]}

Rizzi, Antonello ^{[2
]}

Shafique, Muhammad ^{[3
]}

机构：

[1] Tech Univ Wien TU Wien, Vienna, Austria

[2] Univ Roma La Sapienza, Rome, Italy

[3] New York Univ Abu Dhabi, Div Engn, eBrain Lab, Abu Dhabi, U Arab Emirates

来源：

MICROPROCESSORS AND MICROSYSTEMS | 2023年 / 97卷

关键词：

FPGA; DNA sequence; Inexact string matching; Hardware design; Hardware accelerator; High Level Synthesis; Levenshtein distance; Energy efficiency; Performance;

D O I：

10.1016/j.micpro.2023.104763

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

Since DNA strings suffer from variations like mutation, noisy sampling, and transmission, instead of searching for the exact match, the inexact string matching (ISM) of DNA sequences is preferred. Due to the large amount of data and massive data-dependency, the ISM algorithm is not suitable for being implemented into a general-purpose hardware. Towards this, we propose ISMatch, a novel specialized hardware architecture for computing the ISM in a fast and energy-efficient way. Our implementation on a Xilinx Ultrascale+ FPGA shows up to 70x and 2.2x clock cycles reduction compared to the ARM-based and the HLS implementations, respectively.

引用

页数：10

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