WEIGHTING IN SEQUENCE SPACE - A COMPARISON OF METHODS IN TERMS OF GENERALIZED SEQUENCES
WEIGHTING IN SEQUENCE SPACE - A COMPARISON OF METHODS IN TERMS OF GENERALIZED SEQUENCES
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DOI：
10.1073/pnas.90.19.8777
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发表时间：
1993-10-01
影响因子：
11.1
通讯作者：
SIBBALD, PR
中科院分区：
文献类型：
--
作者：
VINGRON, M;SIBBALD, PR
最近出现了四种用于加权比对的生物序列的方法，它们在数学上、物理上和结果上都不同。因此，虽然对序列加权的必要性有共识，但使用的方法是有争议的。一个连续序列空间的基础上的几何分析，提供了一个共同的框架，比较的方法。最后得出结论，有两个“最好”的方法。当已知序列在遗传学上相关并且可以在不向数据中引入过度应力的情况下生成树时，Altschul等人[Altschul，S. F.、卡罗尔河J. & Lipman，D. J.（1989）J. Mol. Biol.207，647-653]是合适的。当不知道序列在遗传学上是相关的或不能在不过度扭曲序列之间的距离的情况下产生树时，可以修改Sibbald和Argos的方法[Sibbald，P. R. & Argos，P.（1990）J. Mol. Biol. 216，813-818]是优选的。
Four methods for weighting aligned biological sequences have recently appeared that differ mathematically, philosophically, and in their results. Thus, while there is consensus about the need to weight sequences, the method to use is contentious. A geometric analysis based on a continuous sequence space is presented that provides a common framework in which to compare the methods. It is concluded that there are two ''best'' methods. When the sequences are known to be phylogenetically related and a tree can be generated without introducing excessive stress into the data, the method of Altschul et al. [Altschul, S. F., Carroll, R. J. & Lipman, D. J. (1989) J. Mol. Biol. 207, 647-653] is appropriate. When the sequences are not known to be phylogenetically related or a tree cannot be produced without unduly distorting the distances between the sequences, a modification of the method of Sibbald and Argos [Sibbald, P. R. & Argos, P. (1990) J. Mol. Biol. 216, 813-818] is preferable.