用于远缘相关序列比对的基于结构的替换矩阵。

Structure-derived substitution matrices for alignment of distantly related sequences.

作者信息

Prlić A, Domingues F S, Sippl M J

机构信息

Center of Applied Molecular Engineering, Institute for Chemistry and Biochemistry, University of Salzburg, Jakob-Haringerstrasse 3, A-5020 Salzburg, Austria.

出版信息

Protein Eng. 2000 Aug;13(8):545-50. doi: 10.1093/protein/13.8.545.

DOI:10.1093/protein/13.8.545

PMID:10964983

Abstract

Sequence alignment is a standard method to infer evolutionary, structural, and functional relationships among sequences. The quality of alignments depends on the substitution matrix used. Here we derive matrices based on superimpositions from protein pairs of similar structure, but of low or no sequence similarity. In a performance test the matrices are compared with 12 other previously published matrices. It is found that the structure-derived matrices are applicable for comparisons of distantly related sequences. We investigate the influence of evolutionary relationships of protein pairs on the alignment accuracy.

摘要

序列比对是推断序列间进化、结构和功能关系的标准方法。比对的质量取决于所使用的替换矩阵。在这里，我们基于结构相似但序列相似性低或无序列相似性的蛋白质对的叠加来推导矩阵。在性能测试中，将这些矩阵与其他12个先前发表的矩阵进行比较。结果发现，基于结构推导的矩阵适用于远缘相关序列的比较。我们研究了蛋白质对的进化关系对比对准确性的影响。