A survey of multiple sequence alignment techniques

Abstract

Multiple sequence alignment (MSA) is a basic step in many bioinformatics analyses, and also a NP-hard problem. In order to improve the speed, accuracy and cater to the requirement of large-scale sequences alignment, a wide variety of MSA methods and softwares have been subsequently developed. In this article, we will systematically review the wildly used methods and introduce their practical results on the benchmark Balibase 3.0 references. We come to the conclusion that computational complexity still is the bottleneck of MSA. We also consider future development of MSA methods with respect to applying of more different technologies and the prospect of parallelization of MSA. Keywords: Multiple sequence alignment _ MSA techniques