Large scale multiple sequence alignment with simultaneous phylogeny inference

作     者：Parmentier, Gilles Trystram, Denis Zola, Jaroslaw 

作者机构：Lab ID IMAG F-38330 Montbonnot St Martin France Ecole Normale Super Lyon Lab LBMC F-69364 Lyon 07 France 

出 版 物：《JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING》 (并行与分布式计算杂志)

年 卷 期：2006年第66卷第12期

页      面：1534-1545页

核心收录：

学科分类：08[工学] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

主　　题：multiple sequence alignment phylogenctic tree parallel processing distributed caching 

摘      要：Multiple sequence alignment (MSA) and phylogenetic tree reconstruction are one of the most important problems in the computational biology. While both these problems are of great practical significance, in most cases they are very computationally demanding. In this paper we propose a new approach to the MSA problem which simultaneously infers an underlying phylogenetic tree. To process large data sets we provide parallel implementation of our method, which is based on the distributed caching of intermediate results. Finally, we show a parallel server designed for grid environments, and we report results of experiments performed with actual biological data, e.g. 1000 ribosomal RNA sequences. (C) 2006 Elsevier Inc. All rights reserved.