PATTERN-INDUCED MULTI-SEQUENCE ALIGNMENT (PIMA) ALGORITHM EMPLOYING SECONDARY STRUCTURE-DEPENDENT GAP PENALTIES FOR USE IN COMPARATIVE PROTEIN MODELING

被引：231

作者：

SMITH, RF ^{[1
]}

SMITH, TF ^{[1
]}

机构：

[1] HARVARD UNIV, DANA FARBER CANC INST, DEPT BIOSTAT, BOSTON, MA 02115 USA

来源：

PROTEIN ENGINEERING | 1992年 / 5卷 / 01期

关键词：

ALIGNMENTS; HOMOLOGY; MODELING; PROTEIN SEQUENCE; SECONDARY STRUCTURE;

D O I：

10.1093/protein/5.1.35

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：

A multiple sequence alignment algorithm is described that uses a dynamic programming-based pattern construction method to align a set of homologous sequences based on their common pattern of conserved sequence elements. This pattern-induced multi-sequence alignment (PIMA) algorithm can employ secondary-structure dependent gap penalties for use in comparative modelling of new sequences when the three-dimensional structure of one or more members of the same family is known. We show that the use of secondary structure information can significantly improve the accuracy of aligning structure boundaries in a set of homologous sequences even when the structure of only one member of the family is known.

引用

页码：35 / 41

页数：7

共 56 条

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