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An O(n^5) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids

Chen, Ho-Lin and Condon, Anne and Jabbari, Hosna (2009) An O(n^5) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids. Journal of Computational Biology, 16 (6). pp. 803-815. ISSN 1066-5277.

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Efficient methods for prediction of minimum free energy (MFE) nucleic secondary structures are widely used, both to better understand structure and function of biological RNAs and to design novel nano-structures. Here, we present a new algorithm for MFE secondary structure prediction, which significantly expands the class of structures that can be handled in O(n^5) time. Our algorithm can handle H-type pseudoknotted structures, kissing hairpins, and chains of four overlapping stems, as well as nested substructures of these types.

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Additional Information:© 2009 Mary Ann Liebert, Inc. Published in Volume: 16 Issue 6: June 14, 2009. We thank Mirela Andronescu for her input on features of pseudoknotted structures in the RNA STRAND database and Takachi Yokomori for explanations of the structures that can be handled by the algorithm of Uemura et al (1999).
Subject Keywords:kissing hairpins; pseudoknot; RNA; secondary structure prediction
Issue or Number:6
Record Number:CaltechAUTHORS:20090807-121559316
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14871
Deposited By: Jason Perez
Deposited On:07 Aug 2009 20:47
Last Modified:03 Oct 2019 00:53

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