From Serial to Parallel: Enhancing Needleman-Wunsch Performance through GPU-Based Computing

From Serial to Parallel: Enhancing Needleman-Wunsch Performance through GPU-Based Computing

global sequence alignment; GPU computing; Needleman-Wunsch algorithm

The increasing demand for faster bioinformatics analysis calls for more efficient approaches for sequence alignment. In this study, we demonstrate that a GPU-based implementation of the Needleman-Wunsch algorithm can achieve up to 14.8× speedup compared to its traditional CPU-based serial counterpart, without compromising alignment accuracy. By leveraging the parallel processing capabilities and shared memory of an NVIDIA GeForce RTX 3060 Laptop GPU, we significantly accelerated global sequence alignment tasks. Using clinically relevant genes such as NRAS, BRCA1, BRCA2, and Saccharomyces cerevisiae from NCBI ensures realistic alignment challenges and biological significance. Performance evaluation across a wide range of sequence lengths demonstrates the scalability and efficiency of the parallel approach. More importantly, this study provides a unique contribution by showing that a commodity GPU, such as the NVIDIA GeForce RTX 3060 Laptop, can serve as a practical alternative when high-performance computing clusters are unavailable or prohibitively expensive, thereby offering an accessible and cost-effective pathway to high-throughput bioinformatics workflows.

Yustina Sri Suharini1, Wisnu Ananta Kusuma2, Sri Nurdiati3, Irmanida Batubara4

https://jurnal.iaii.or.id/index.php/RESTI/article/view/6620/1156

2Department of Computer Science, School of Data Science, Mathematics and Informatics, IPB University, Bogor, Indonesia

October 25, 2025

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