This article is part of the supplement: Selected articles from the First IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS 2011): Bioinformatics

Open Access Research

Accelerating pairwise statistical significance estimation for local alignment by harvesting GPU's power

Yuhong Zhang12*, Sanchit Misra2, Ankit Agrawal2, Md Mostofa Ali Patwary2, Wei-keng Liao2, Zhiguang Qin1 and Alok Choudhary2

Author Affiliations

1 School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China

2 Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, USA

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BMC Bioinformatics 2012, 13(Suppl 5):S3  doi:10.1186/1471-2105-13-S5-S3

Published: 12 April 2012



Pairwise statistical significance has been recognized to be able to accurately identify related sequences, which is a very important cornerstone procedure in numerous bioinformatics applications. However, it is both computationally and data intensive, which poses a big challenge in terms of performance and scalability.


We present a GPU implementation to accelerate pairwise statistical significance estimation of local sequence alignment using standard substitution matrices. By carefully studying the algorithm's data access characteristics, we developed a tile-based scheme that can produce a contiguous data access in the GPU global memory and sustain a large number of threads to achieve a high GPU occupancy. We further extend the parallelization technique to estimate pairwise statistical significance using position-specific substitution matrices, which has earlier demonstrated significantly better sequence comparison accuracy than using standard substitution matrices. The implementation is also extended to take advantage of dual-GPUs. We observe end-to-end speedups of nearly 250 (370) × using single-GPU Tesla C2050 GPU (dual-Tesla C2050) over the CPU implementation using Intel© Core™i7 CPU 920 processor.


Harvesting the high performance of modern GPUs is a promising approach to accelerate pairwise statistical significance estimation for local sequence alignment.