GAP COSTS FOR MULTIPLE SEQUENCE ALIGNMENT
GAP COSTS FOR MULTIPLE SEQUENCE ALIGNMENT
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DOI：
10.1016/s0022-5193(89)80196-1
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发表时间：
1989-06-08
影响因子：
2
通讯作者：
ALTSCHUL, SF
中科院分区：
文献类型：
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作者：
ALTSCHUL, SF
比对生物序列对的标准方法负责最常见的突变，即替换、删除和插入。由于单个突变可能插入或删除多个核苷酸，因此与间隙长度不成正比的间隙成本通常是最有效的。如何将这种缺口成本扩展到三个或更多序列的比对并不是立即显而易见的，并且已经采取了多种方法。本文认为，由于差距和替代成本共同指定了最佳排列，因此应该使用共同的基本原理来定义它们。具体来说，提出了多重比对的间隙成本的新定义，并与以前的定义进行了比较。由于新定义将多重比对的成本与其成对投影的成本联系起来，因此它允许获得有关双序列比对的知识来解决多重比对问题。此外，这种连接是最近算法的关键要素，该算法已经使多达六个序列的模拟比对变得实用。
Standard methods for aligning pairs of biological sequences charge for the most common mutations, which are substitutions, deletions and insertions. Because a single mutation may insert or delete several nucleotides, gap costs that are not directly proportional to gap length are usually the most effective. How to extend such gap costs to alignments of three or more sequences is not immediately obvious, and a variety of approaches have been taken. This paper argues that, since gap and substitution costs together specify optimal alignments, they should be defined using a common rationale. Specifically, a new definition of gap costs for multiple alignments is proposed and compared with previous ones. Since the new definition links a multiple alignment''s cost to that of its pairwise projections, it allows knowledge gained about two-sequence alignments to bear on multiple alignment problem. Also, such linkage is a key element of recent algorithms that have rendered practical the simulations alignment of as many as six sequences.