TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots

被引：14

作者：

Seetin, Matthew G. ^{[1
]}

Mathews, David H. ^{[1
,2
]}

机构：

[1] Univ Rochester, Med Ctr, Dept Biochem & Biophys, Ctr RNA Biol, Rochester, NY 14642 USA

[2] Univ Rochester, Med Ctr, Dept Biostat & Computat Biol, Rochester, NY 14642 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 06期

基金：

美国国家卫生研究院;

关键词：

DYNAMIC-PROGRAMMING ALGORITHM; PARTITION-FUNCTION; THERMODYNAMIC PARAMETERS; PROBABILISTIC ALIGNMENT; SEQUENCE ALIGNMENT; CONSTRAINTS; ACCURACY; GRAMMARS; COMMON; MODEL;

D O I：

10.1093/bioinformatics/bts044

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Many RNA molecules function without being translated into proteins, and function depends on structure. Pseudoknots are motifs in RNA secondary structures that are difficult to predict but are also often functionally important. Results: TurboKnot is a new algorithm for predicting the secondary structure, including pseudoknotted pairs, conserved across multiple sequences. TurboKnot finds 81.6% of all known base pairs in the systems tested, and 75.6% of predicted pairs were found in the known structures. Pseudoknots are found with half or better of the false-positive rate of previous methods.

引用

页码：792 / 798

页数：7

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