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Topology and prediction of RNA pseudoknots

Reidys, Christian M. and Huang, Fenix W. D. and Andersen, Jørgen E. and Penner, Robert C. and Stadler, Peter F. and Nebel, Markus E. (2011) Topology and prediction of RNA pseudoknots. Bioinformatics, 27 (8). pp. 1076-1085. ISSN 1367-4803.

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Motivation: Several dynamic programming algorithms for predicting RNA structures with pseudoknots have been proposed that differ dramatically from one another in the classes of structures considered. Results: Here, we use the natural topological classification of RNA structures in terms of irreducible components that are embeddable in the surfaces of fixed genus. We add to the conventional secondary structures four building blocks of genus one in order to construct certain structures of arbitrarily high genus. A corresponding unambiguous multiple context-free grammar provides an efficient dynamic programming approach for energy minimization, partition function and stochastic sampling. It admits a topology-dependent parametrization of pseudoknot penalties that increases the sensitivity and positive predictive value of predicted base pairs by 10–20% compared with earlier approaches. More general models based on building blocks of higher genus are also discussed.

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Additional Information:© The Author 2011. Published by Oxford University Press. Received October 14, 2010; Revision received January 12, 2011; Accepted February 15, 2011. First published online: February 17, 2011. This work was supported by the 973 Project of the Ministry of Science and Technology; the PCSIRT Project of the Ministry of Education; National Science Foundation of China to C.M.R. and his lab; Deutsche Forschungsgemeinschaft (projects STA 850/2-1 & STA850/7-1); the European Union FP-7 project QUANTOMICS (no. 222664) to P.F.S. and his lab. J.E.A. and R.C.P. are supported by QGM, the Centre for Quantum Geometry of Moduli Spaces, funded by the Danish National Research Foundation. Conflict of Interest: none declared.
Funding AgencyGrant Number
Ministry of Science and Technology 973 ProjectUNSPECIFIED
Ministry of Education PCSIRT ProjectUNSPECIFIED
National Science Foundation of ChinaUNSPECIFIED
Deutsche ForschungsgemeinschaftSTA 850/2-1
Deutsche ForschungsgemeinschaftSTA850/7-1
European Union FP-7 project QUANTOMICS222664
Danish National Research Foundation Centre for Quantum Geometry of Moduli Spaces (QGM)UNSPECIFIED
Issue or Number:8
Record Number:CaltechAUTHORS:20110429-103523602
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:23498
Deposited By: Jason Perez
Deposited On:02 May 2011 16:53
Last Modified:03 Oct 2019 02:47

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