Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges
Theoretical Computer Science
Fast prediction of RNA-RNA interaction
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Time and space efficient RNA-RNA interaction prediction via sparse folding
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
| Hi-index | 3.84 |
Background: Reliable prediction of RNA--RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA--mRNA binding and antisense interactions. The thermodynamics of such RNA--RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to 'open' the binding site and (2) the energy gained from hybridization. Methods: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired. Results: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable with a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target. Availability: RNAup will be distributed as part of the Vienna RNA Package, www.tbi.univie.ac.at/~ivo/RNA/ Contact: ivo@tbi.univie.ac.at