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Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs

Songwen Pei, Wenhao Wang, Gang Wei, Baifeng Wu
Department of Computer Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
Journal of Computational Information Systems 7:4, p.1246-1253, 2011

@article{pei2011large,

   title={Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs},

   author={PEI, S. and WANG, W. and WEI, G. and WU, B.},

   journal={Journal of Computational Information Systems},

   volume={7},

   number={4},

   pages={1246–1253},

   year={2011}

}

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Large Scale DNA sequence alignment and Kernel method in molecular biology play critical roles in bioinformatics. Both of which are successfully implemented on the brook+ platform with AMD’s GPUs. Aiming at the characters of graphical stream processors, we propose internal and external approach cooperatively to promote the performance of the two algorithms. The experiments show that the performance of 2D graph-based DNA sequence alignment based on GPUs is more than 25x faster than that of a single CPU-based one, and the parallel kernel matrix computing runs 7x faster on the same platform due to the write-back bottleneck of graph memory which simultaneously reveals the limitation of GPUs computing.
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