Prediction of consensus RNA secondary structures including pseudoknots

被引：40
|
作者：
Witwer, C
Hofacker, IL
Stadler, PF
机构：
[1] Univ Vienna, Inst Theoret Chem & Mol Strukturbiol, A-1090 Vienna, Austria
[2] Univ Leipzig, Inst Informat, Lehrstuhl Bioinformat, D-04103 Leipzig, Germany
来源：
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS | 2004年 / 1卷 / 02期
关键词：
RNA secondary structure; pseudoknots; covariance;
D O I：
10.1109/TCBB.2004.22
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here, we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm. We applied our algorithm to a number of different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly and more than 85 percent of the base pairs were identified.
引用
收藏
页码：66 / 77
页数：12
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