Blogel-SPINAL：分布式PPI网络比对算法

TP393; 高通量技术的发展使蛋白质-蛋白质相互作用(PPI)网络的规模日益增大,需要高速算法对其进行全局比对.为此,分析集中式全局比对算法SPINAL,将该算法中耗时超过95％的计算估计值阶段移植到分布式平台Blogel下运算,求比对图阶段则仍保持集中式运算,以此得到Blogel-SPINAL算法.理论分析和实验结果表明,与SPINAL相比,Blogel-SPINAL能提升比对速度,具有较好的扩展性....

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Bibliographic Details
Published in计算机工程 Vol. 42; no. 4; pp. 209 - 214
Main Author 周文剑 靳婷
Format Journal Article
LanguageChinese
Published 复旦大学计算机科学技术学院,上海,200433%海南大学信息科学技术学院,海口,570228 2016
Subjects
全局网络比对
分布式计算
可扩展性
积图
蛋白质-蛋白质相互作用网络
顶点划分
积图
global network alignment
蛋白质-蛋白质相互作用网络
分布式计算
顶点划分
可扩展性
distributed computation
全局网络比对
product graph
Protein-protein Interaction (PPI) network
scalability
vertex partition
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ISSN1000-3428
DOI10.3969/j.issn.1000-3428.2016.04.037

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Summary:TP393; 高通量技术的发展使蛋白质-蛋白质相互作用(PPI)网络的规模日益增大,需要高速算法对其进行全局比对.为此,分析集中式全局比对算法SPINAL,将该算法中耗时超过95％的计算估计值阶段移植到分布式平台Blogel下运算,求比对图阶段则仍保持集中式运算,以此得到Blogel-SPINAL算法.理论分析和实验结果表明,与SPINAL相比,Blogel-SPINAL能提升比对速度,具有较好的扩展性.
Bibliography:31-1289/TP
ZHOU Wenjian,JIN Ting（1. School of Computer Science, Fudan University, Shanghai 200433, China ; 2. College of Information Science and Technology, Hainan University, Haikou 570228, China）
distributed computation; Protein-protein Interaction （ PPI ） network; global network alignment ; product graph ; vertex partition ; scalability
With the development of high throughput technology, the size of Protein-protein Interaction （PPI） network grows larger and larger,thus high speed PPI network global alignment algorithm is needed. Aiming at this problem, this paper analyzes the SPINAL algorithm. It modifies the coarse-grained phase which occupies more than 95% time cost to adapt for distributed platform named Blogel, and keeps the fine-grained phase unchanged. Hence, the Blogel-SPINAL algorithm is gotten. Theoretical analysis and experimental results show that Blogel-SPINAL is much faster than SPINAL, and its scalability is better.
ISSN:1000-3428
DOI:10.3969/j.issn.1000-3428.2016.04.037