Prediction of consensus RNA secondary structures including pseudoknots

Author

Witwer, Christina ; Hofacker, Ivo L. ; Stadler, Peter F.

Volume

1

Issue

2

fYear

2004

Firstpage

66

Lastpage

77

Abstract

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.

Keywords

biology computing; macromolecules; molecular biophysics; molecular configurations; thermodynamics; base pairs; consensus RNA secondary structures; covariation information; functional RNA molecules; maximum weighted matching algorithm; pseudoknots; sequence alignments; thermodynamics; Biology computing; Computational biology; Mutual information; Polynomials; Predictive models; Quantum computing; RNA; Sequences; Thermodynamics; Uncertainty; Index Terms- RNA secondary structure; covariance.; pseudoknots; Algorithms; Base Pairing; Base Sequence; Computational Biology; Models, Molecular; Nucleic Acid Conformation; RNA; RNA, Bacterial; Sequence Alignment; Thermodynamics;

fLanguage

English

Journal_Title

Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Publisher

ieee

ISSN

1545-5963

Type

jour

DOI

10.1109/TCBB.2004.22

Filename

1350749