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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| Veröffentlicht in: | IEEE/ACM transactions on computational biology and bioinformatics 2004-04, Vol.1 (2), p.66-77 |
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| container_title | IEEE/ACM transactions on computational biology and bioinformatics |
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| creator | Witwer, C. Hofacker, I.L. Stadler, P.F. |
| description | 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. |
| doi_str_mv | 10.1109/TCBB.2004.22 |
| format | Article |
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| 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 |
| title | Prediction of consensus RNA secondary structures including pseudoknots |
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