Structure-derived substitution matrices for alignment of distantly related sequences

被引：72

作者：

Prlic, A ^{[1
]}

Domingues, FS ^{[1
]}

Sippl, MJ ^{[1
]}

机构：

[1] Salzburg Univ, Inst Chem & Biochem, Ctr Appl Mol Engn, A-5020 Salzburg, Austria

来源：

PROTEIN ENGINEERING | 2000年 / 13卷 / 08期

关键词：

alignment accuracy; protein evolution; sequence alignment; structure alignment; substitution matrix;

D O I：

10.1093/protein/13.8.545

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：545 / 550

页数：6