Prediction of consensus RNA secondary structures including pseudoknots

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 a...

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Bibliographic Details
Published in:IEEE/ACM transactions on computational biology and bioinformatics 2004-04, Vol.1 (2), p.66-77
Main Authors: Witwer, C., Hofacker, I.L., Stadler, P.F.
Format: Article
Language:English
Subjects:
Algorithms
Base Pairing
Base Sequence
Biology computing
Computational biology
Computational Biology - methods
covariance
Index Terms- RNA secondary structure
Models, Molecular
Mutual information
Nucleic Acid Conformation
Polynomials
Predictive models
pseudoknots
Quantum computing
RNA
RNA - chemistry
RNA, Bacterial - chemistry
Sequence Alignment - statistics & numerical data
Sequences
Thermodynamics
Uncertainty
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Description
Summary: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.
ISSN:1545-5963
1557-9964
DOI:10.1109/TCBB.2004.22