Pairwise Sequence Alignment for Very Long Sequences on GPUs.

IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences Pub Date : 2012-01-01 DOI:10.1109/ICCABS.2012.6182641

Junjie Li, Sanjay Ranka, Sartaj Sahni

引用次数: 22

Abstract

We develop novel single-GPU parallelizations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignment score as well as the actual alignment. Experimental results demonstrate an order of magnitude reduction in run time relative to competing GPU algorithms.

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gpu上超长序列的成对序列对齐。

我们开发了新的单gpu并行史密斯-沃特曼算法成对序列对齐。我们的算法适用于单对超长序列的比对，可以用来确定比对得分和实际比对。实验结果表明，相对于竞争的GPU算法，该算法的运行时间减少了一个数量级。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences

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