多序列渐进式比对算法研究与比较  

Study and comparison of multiple sequence progressive alignment algorithms

作　　者：谷俊峰[1] 王希诚[1] 赵金城[2] 

机构地区：[1]大连理工大学工业装备结构分析国家重点实验室,大连116023 [2]大连大学生物信息学与分子设计研究所,大连116622

出　　处：《生物信息学》2005年第2期73-76,共4页Chinese Journal of Bioinformatics

基　　金：国家重点基础研究发展规划项目(No.2004CB518901);国家自然科学基金(No.10272030)

摘　　要：多序列比对是一种重要的生物信息学工具,在生物的进化分析以及蛋白质的结构预测方面有着重要的应用。以ClustalW为代表的渐进式多序列比对算法在这个领域取得了很大的成功,成为应用最为广泛的多序列比对程序。但其固有的缺陷阻碍了比对精度的进一步提高,近年来出现了许多渐进式比对算法的改进算法,并取得良好的效果。本文选取了其中比较有代表性的几种算法对其基本比对思想予以描述,并且利用多序列比对程序平台BAliBASE和仿真程序ROSE对它们的精度和速度分别进行了比较和评价。Multiple sequence alignment is one of the essential tools of studying bioinformatics and it plays an important role in the evolution analysis and protein structure prediction. Multiple sequence progressive alignment algorithms, represented by Custal W has achieved great success in this research field, making it most widely applied. However, the inherent disadvantage of the program has encumbered further improvement of alignment efficiency. In recent years many improved progressive methods were then developed and received good results. In this article, some of the representatives of the methods are selected and their basic ideas are sketched. The efficiency and speed of these methods are also compared and evaluated through using BAliBASE and simulation program ROSE.

关 键 词：渐进式 算法研究 多序列比对 序列比对算法 生物信息学 结构预测 进化分析 改进算法 ROSE 仿真程序 蛋白质 代表性 应用 精度 

分 类 号：TP301.6[自动化与计算机技术—计算机系统结构] F121[自动化与计算机技术—计算机科学与技术]