Efficient RNA pairwise structure comparison by SETTER method
Efficient RNA pairwise structure comparison by SETTER method
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DOI：
10.1093/bioinformatics/bts301
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发表时间：
2012-07-15
期刊：
影响因子：
5.8
通讯作者：
Svozil, Daniel
中科院分区：
文献类型：
--
作者：
Hoksza, David;Svozil, Daniel
动机：了解RNA分子的结构和功能需要比较和分析其3D结构的方法。尽管短RNA的结构比对可以在合理的时间内实现，但大型结构面临着更大的挑战。然而，存储在PDB数据库中的大量RNA数量的增长要求开发快速、准确的结构分析方法，以及在数据库中快速进行相似性搜索。结果：本文提出了一种新的RNA结构比较设置算法(基于二级结构的三级结构相似性算法)。Setter使用基于所谓广义二级结构单元的三维相似性的成对比较方法。对于每一对结构，setter都会生成一个距离分数，并指示其统计意义。Setter既可用于已知同源结构的结构比对，也可用于3D结构相似性搜索和功能注释。该算法既准确又快速，并且不对排列的RNA结构的大小施加限制。
Motivation: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their 3D structures. Although a structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. However, the growth of the number of large RNAs deposited in the PDB database calls for the development of fast and accurate methods for analyzing their structures, as well as for rapid similarity searches in databases.Results: In this article a novel algorithm for an RNA structural comparison SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) is introduced. SETTER uses a pairwise comparison method based on 3D similarity of the so-called generalized secondary structure units. For each pair of structures, SETTER produces a distance score and an indication of its statistical significance. SETTER can be used both for the structural alignments of structures that are already known to be homologous, as well as for 3D structure similarity searches and functional annotation. The algorithm presented is both accurate and fast and does not impose limits on the size of aligned RNA structures.