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Partition function and base pairing probabilities of RNA heterodimers (2006)
| Venue: | Algorithms Mol Biol |
| Citations: | 65 - 14 self |
BibTeX
@ARTICLE{Bernhart06partitionfunction,
author = {Stephan H Bernhart and Hakim Tafer and Christoph Flamm and Peter F Stadler and Ivo L Hofacker},
title = {Partition function and base pairing probabilities of RNA heterodimers},
journal = {Algorithms Mol Biol},
year = {2006},
pages = {2006}
}
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Abstract
Abstract Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, noncoding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods: The standard dynamic programming algorithms for computing secondary structures of linear singlestranded RNA molecules are extended to the co-folding of two interacting RNAs. Results: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.
Keyphrases
base pairing probability partition function rna heterodimers rna molecule ground state complex internal structure equilibrium concentration cellular regulation realistic interaction energy energy band inter-molecular base pairing abstract background minimum energy structure target prediction algorithm duplex structure base pairing pattern interaction derives hybridization energy many case suboptimal structure partition function algorithm secondary structure recent year accurate computational treatment key player standard dynamic programming algorithm complete set nucleic acid
