.png){kind=icon}
返回
DNA fragment assembly using a grid-based genetic algorithm
.png){kind=icon}
PRE
AI
DOI：10.1016/j.cor.2006.12.011.png)
.png){kind=icon}
原文求助.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
In this paper we propose a genetic algorithm (GA) for solving the DNA fragment assembly problem in a computational grid. The algorithm, which is named GrEA, is a steady-state GA which uses a panmitic population, and it is based on computing parallel function evaluations in an asynchronous way. We have implemented GrEA on top of the Condor system, and we have used it to solve the DNA assembly problem. This is an NP-hard combinatorial optimization problem which is growing in importance and complexity as more research centers become involved on sequencing new genomes. While previous works on this problem have usually faced 30 K base pairs (bps) long instances, we have tackled here a 77 K bps long one to show how a grid system can move research forward. After analyzing the basic grid algorithm, we have studied the use of an improvement method to still enhance its scalability. Then, by using a grid composed of up to 150 computers, we have achieved time reductions from tens of days down to a few hours, and we have obtained near optimal solutions when solving the 77 K bps long instance (773 fragments). We conclude that our proposal is a promising approach to take advantage of a grid system to solve large DNA fragment assembly problem instances and also to learn more about grid metaheuristics as a new class of algorithms for really challenging problems. (c) 2007 Elsevier Ltd. All rights reserved.
Keyword:
DNA fragment assembly
grid computing
genetic algorithm
AI总结
对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。
期刊
C
IF:
4.3
论文数:
6.5K
被引数:
1.8W
机构
引用论文
The Horner–Wadsworth–Emmons reaction of mixed phosphonoacetates and aromatic aldehydes: geometrical selectivity and computational investigation.png)
Tetrahedron
TetrahedronIF0
PREAI
分享收藏
分享收藏Predicting seasonal diet in the yellow-bellied marmot: success and failure for the linear programming modelOecologia
OecologiaIF0
PREAI
分享收藏分享收藏
查看更多内容