Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.
复制标题
DOI：
10.1186/1471-2105-12-221
复制
发表时间：
2011-06-01
影响因子：
3
通讯作者：
Rognes T
中科院分区：
文献类型：
--
作者：
Rognes T
Smith-Waterman局部序列比对算法比启发式数据库搜索算法更敏感，但也更耗时。使用SIMD技术的最快并行化方法先前由Farrar在2007年描述。本研究的目的是探讨是否可以通过其他方法来获得进一步的速度并行化。一个更快的方法和实施的描述和基准。在新工具SWIPE中，来自16个不同数据库序列的残基与一个查询残基平行比较。使用375个残基查询序列，在双Intel Xeon X5650六核处理器系统上实现了每秒1060亿次单元更新（GCUPS）的速度，这比基于Farrar 'striped'方法的软件快六倍以上。当程序只使用一个线程时，SWIPE的速度大约是2.5倍。对于较短的查询，速度的提高更大。当使用BLOSUM 50评分矩阵时，SWIPE大约是BLAST的两倍，而对于BLOSUM 62矩阵，BLAST大约是SWIPE的两倍。该软件专为SSSE 3处理器上的64位Linux设计。源代码可以在GNU Affero通用公共许可证下从http://dna.uio.no/swipe/获得。在标准硬件上使用SIMD的高效并行化使得Smith-Waterman数据库搜索的速度比以前快六倍以上。这里描述的方法可以显着扩大史密斯-沃特曼搜索的潜在应用。其他需要最佳局部比对分数的应用也可以从改进的性能中受益。
The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.
登录
查看更多内容
影响因子：
1.8
作者：
Szalkowski A;Ledergerber C;Krähenbühl P;Dessimoz C
通讯作者：
Dessimoz C
DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
5.8
作者：
Rognes, T;Seeberg, E
通讯作者：
Seeberg, E
影响因子：
4.3
作者：
Rumble SM;Lacroute P;Dalca AV;Fiume M;Sidow A;Brudno M
通讯作者：
Brudno M
影响因子：
4.4
作者：
Miller, Jason R.;Koren, Sergey;Sutton, Granger
通讯作者：
Sutton, Granger