多序列渐进式比对算法研究与比较

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。

Study and comparison of multiple sequence progressive alignment algorithms

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.