SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2.
SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2.
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DOI：
10.1186/1756-0500-1-107
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发表时间：
2008-10-29
影响因子：
1.8
通讯作者：
Dessimoz C
中科院分区：
文献类型：
--
作者：
Szalkowski A;Ledergerber C;Krähenbühl P;Dessimoz C
我们提出了swps 3，一个矢量化的实现的Smith-Waterman局部对齐算法优化的细胞/BE和×86架构。本文介绍了swps 3，并与其他几种实现的性能进行了比较。我们的基准测试结果表明，swps 3是目前在Cell/BE上实现矢量化Smith-Waterman的最快实现，比其他唯一已知的实现至少高出4倍：在PlayStation 3上，它实现了高达每秒80亿次单元更新（GCUPS）。使用SSE 2指令集，一个四核Intel Pentium可以达到15.7 GCUPS。我们还表明，在这个CPU上的swps 3比最近的GPU实现更快。最后，我们注意到，在某些情况下，比对的计算速度与BLAST（一种启发式方法）大致相同。Cell/BE可以成为比对生物序列的强大平台。此外，精确方法和启发式方法之间的性能差距几乎已经消失，特别是对于长蛋白质序列。
We present swps3, a vectorized implementation of the Smith-Waterman local alignment algorithm optimized for both the Cell/BE and ×86 architectures. The paper describes swps3 and compares its performances with several other implementations. Our benchmarking results show that swps3 is currently the fastest implementation of a vectorized Smith-Waterman on the Cell/BE, outperforming the only other known implementation by a factor of at least 4: on a Playstation 3, it achieves up to 8.0 billion cell-updates per second (GCUPS). Using the SSE2 instruction set, a quad-core Intel Pentium can reach 15.7 GCUPS. We also show that swps3 on this CPU is faster than a recent GPU implementation. Finally, we note that under some circumstances, alignments are computed at roughly the same speed as BLAST, a heuristic method. The Cell/BE can be a powerful platform to align biological sequences. Besides, the performance gap between exact and heuristic methods has almost disappeared, especially for long protein sequences.