A Guide to Parallel Execution of Sequence Alignment

被引：0

作者：

Lauredo, Alexandre M. ^{[1
]}

Sena, Alexandre C. ^{[1
]}

de Castro, Maria Clicia S. ^{[1
]}

Marzulo, Leandro A. J. ^{[1
]}

机构：

[1] Univ Estado Rio De Janeiro, Inst Math & Stat, Rio De Janeiro, Brazil

来源：

PROCEEDINGS OF THE INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2016 (ICCMSE-2016) | 2016年 / 1790卷

关键词：

High Performance Computing; Multicore Clusters; Sequence Alignment;

D O I：

10.1063/1.4968702

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

Finding the longest common subsequence (LCS) is an important part of DNA sequence alignment. Through dynamic programming it is possible to find the exact solution to the LCS, with space and time complexity of O(m x n), being m e n the sequence sizes. Parallel algorithms are essential, since large sequences require too much time and memory to be processed sequentially. Thus, the aim of this work is to implement and evaluate different parallel solutions for distributed memory machines, so that the amount of memory is equally divided among the various processing nodes.

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