Parallelizing exact motif finding algorithms on multi-core

被引：0
|
作者：
Mostafa M. Abbas
Hazem M. Bahig
Mohamed Abouelhoda
M. M. Mohie-Eldin
机构：
[1] Qatar University,KINDI Lab for Computing Research, College of Engineering
[2] Sinai University,Department of Basic Sciences, Faculty of Engineering
[3] Hail University,Computer Science and Software Engineering Department, College of Computer Science and Engineering
[4] Ain Shams University,Computer Science Division, Department of Mathematics, Faculty of Science
[5] Cairo University,Systems and Biomedical Engineering Department, Faculty of Engineering
[6] Nile University,Center for Informatics Sciences
[7] Al-Azhar University,Department of Mathematics, Faculty of Science
来源：
The Journal of Supercomputing | 2014年 / 69卷
关键词：
Exact algorithms; Motif finding; Multi-core; Challenging and solvable instances;
D O I：
暂无
中图分类号：
学科分类号：
摘要：
The motif finding problem is one of the important and challenging problems in bioinformatics. A variety of sequential algorithms have been proposed to find exact motifs, but the running time is still not suitable due to high computational complexity of finding motifs. In this paper we parallelize three efficient sequential algorithms which are HEPPMSprune, PMS5 and PMS6. We implement the algorithms on a Dual Quad-Core machine using openMP to measure the performance of each algorithm. Our experiment on simulated data show that: (1) the parallel PMS6 is faster than the other algorithms in case of challenging instances, while the parallel HEPPMSprune is faster than the other algorithms in most of solvable instances; (2) the scalability of parallel HEPPMSprune is linear for all instances, while the scalability of parallel PMS5 and PMS6 is linear in case of challenging instances only; (3) the memory used by HEPPMSprune is less than that of the other algorithms.
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收藏
页码：814 / 826
页数：12
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