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GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences

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In this paper, we present GSWABE, a graphics processing unit GPU-accelerated pairwise sequence alignment algorithm for a collection of short DNA sequences. This algorithm supports all-to-all pairwise global, semi-global and local alignment, and retrieves optimal alignments on Compute Unified Device Architecture CUDA-enabled GPUs. All of the three alignment types are based on dynamic programming and share almost the same computational pattern. Thus, we have investigated a general tile-based approach to facilitating fast alignment by deeply exploring the powerful compute capability of CUDA-enabled GPUs. The performance of GSWABE has been evaluated on a Kepler-based Tesla K40 GPU using a variety of short DNA sequence datasets. The results show that our algorithm can yield a performance of up to 59.1 billions cell updates per second GCUPS, 58.5 GCUPS and 50.3 GCUPS for global, semi-global and local alignment, respectively. Furthermore, on the same system GSWABE runs up to 156.0 times faster than the Streaming SIMD Extensions SSE-based SSW library and up to 102.4 times faster than the CUDA-based MSA-CUDA the first stage in terms of local alignment. Compared with the CUDA-based gpu-pairAlign, GSWABE demonstrates stable and consistent speedups with a maximum speedup of 11.2, 10.7, and 10.6 for global, semi-global, and local alignment, respectively. Copyright © 2014 John Wiley & Sons, Ltd.