Partition function and base pairing probabilities of RNA heterodimers 英文参考文献.docVIP

Algorithms for Molecular Biology BioMedCentral Research Open Access Partition function and base pairing probabilities of RNA heterodimers Stephan H Bernhart*1, Hakim Tafer1, Ulrike Mückstein1, Christoph Flamm2,1, Peter F Stadler2,1,3 and Ivo L Hofacker1 Address: 1Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, W?hringerstrasse 17, Vienna, Austria, 2Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, H?rtelstrasse 16– 18, D-04170 Leipzig, Germany and 3The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, New Mexico Email: Stephan H Bernhart* - berni@tbi.univie.ac.at; Hakim Tafer - htafer@tbi.univie.ac.at; Ulrike Mückstein - ulim@tbi.univie.ac.at; Christoph Flamm - xtof@tbi.univie.ac.at; Peter F Stadler - studla@tbi.univie.ac.at; Ivo L Hofacker - ivo@tbi.univie.ac.at * Corresponding author Published: 16 March 2006 Received: 16 February 2006 Accepted: 16 March 2006 Algorithms for Molecular Biology2006, 1:3 doi:10.1186/1748-7188-1-3 This article is available from: /content/1/1/3 ? 2006Bernhart et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding 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 sing