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Target prediction and a statistical sampling algorithm for RNA-RNA interaction

: Huang, F.W.D.; Qin, J.; Reidys, C.M.; Stadler, P.F.


Bioinformatics 26 (2010), No.2, pp.175-181
ISSN: 1367-4803
ISSN: 1460-2059
Journal Article
Fraunhofer IZI ()

Motivation: It has been proven that the accessibility of the target sites has a critical influence on RNA-RNA binding, in general and the specificity and efficiency of miRNAs and siRNAs, in particular. Recently, O(N-6) time and O(N-4) space dynamic programming (DP) algorithms have become available that compute the partition function of RNA-RNA interaction complexes, thereby providing detailed insights into their thermodynamic properties. Results: Modifications to the grammars underlying earlier approaches enables the calculation of interaction probabilities for any given interval on the target RNA. The computation of the 'hybrid probabilities' is complemented by a stochastic sampling algorithm that produces a Boltzmann weighted ensemble of RNA-RNA interaction structures. The sampling of k structures requires only negligible additional memory resources and runs in O(k.N-3).