Segment-based multiple sequence alignment
Segment-based multiple sequence alignment
复制标题
DOI：
10.1093/bioinformatics/btn281
复制
发表时间：
2008-08-15
期刊：
影响因子：
5.8
通讯作者：
Reinert, Knut
中科院分区：
文献类型：
--
作者：
Rausch, Tobias;Emde, Anne-Katrin;Reinert, Knut
动机：过去已经开发了许多多序列比对工具，无论是在速度上还是在比对精度上都有所进步。鉴于比对工具的重要性和广泛使用，这两个类别的进展都是对社区的贡献，并推动了该领域的研究。结果：我们引入了基于一致性的渐进式比对策略的基于图形的扩展。我们将一致性概念应用于分段，而不是单个字符。我们在这种情况下解决的主要问题是以一种基于图的比对可能的方式来定义序列的片段。我们使用SeqAn文库实现了该算法，并报告了氨基酸和DNA序列的结果。我们的方法有三个好处：(1)具有保守区块的序列可以快速比对；(2)概念上实现容易、通用和快速；(3)一致性思想可以扩展到比对多个基因组序列。
Motivation: Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use of alignment tools, progress in both categories is a contribution to the community and has driven research in the field so far.Results: We introduce a graph-based extension to the consistency-based, progressive alignment strategy. We apply the consistency notion to segments instead of single characters. The main problem we solve in this context is to define segments of the sequences in such a way that a graph-based alignment is possible. We implemented the algorithm using the SeqAn library and report results on amino acid and DNA sequences. The benefit of our approach is threefold: (1) sequences with conserved blocks can be rapidly aligned, (2) the implementation is conceptually easy, generic and fast and (3) the consistency idea can be extended to align multiple genomic sequences.