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

Abstract

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 70× and 2.2× clock cycles reduction compared to the ARM-based and the HLS implementations, respectively.