Harnessing GPU Acceleration for Exact DNA Sequence Matching via the KMP Algorithm

Beatrice Branchini, Pierluigi Negro, Ian Di Dio Lavore, Marco D. Santambrogio

Abstract: Identifying recurrent patterns and mutations in the DNA is essential for helping clinicians formulate faster diagnoses and develop personalized treatments. Here, exact matching represents a core procedure. However, due to its computational intensity, it embodies a bottleneck in many genome analysis pipelines. In this context, the computational efficiency of the chosen algorithm used for exact matching combined with the GPUs’ computing power is crucial to speeding up the process. This paper introduces a high-performance multi-GPU solution for exact DNA sequence matching based on the Knuth-Morris-Pratt (KMP) algorithm, designed to identify all possible occurrences of patterns within a reference DNA. Our solution offers a multi-pattern search that exploits multi-buffering to maximize data reuse and overlap data transfers with computation. Experimental results show that our approach for the KMP algorithm attains 5.83× over a state-of-the-art software for genome analysis. Also, our solution run on an AMD MI210 attains up to 1.59 over the best-performing FPGA solution in the literature. ×