Journal
BIOINFORMATICS
Volume 26, Issue 2, Pages 175-181Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btp635
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Funding
- Ministry of Science and Technology
- Ministry of Education
- National Science Foundation of China
- Deutsche Forschungsgemeinschaft [STA 850/7-1]
- European Community [043312]
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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).
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