K-partite RNA secondary structures

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Minghui JiangD Scott Fechser

Abstract

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k pseudoknot-free sub-structures. Most known RNA secondary structures are either bipartite or tripartite. We show that there exists a constant number k such that any secondary structure can be modified into a k-partite secondary structure with approximately the same free energy. This offers a partial explanation of the prevalence of k-partite secondary structures with small k. We give a complete characterization of the computational complexities of recognizing k-partite secondary structures for all k > or = 2, and show that this recognition problem is essentially the same as the k-colorability problem on circle graphs. We present two simple heuristics, iterated peeling and first-fit packing, for finding k-partite RNA secondary structures. For maximizing the number of base pair stackings, our iterated peeling heuristic achieves a constant appr...Continue Reading

References

Nov 14, 1973·Nature: New Biology·I TinocoJ Bralla
Jun 7, 1995·Journal of Theoretical Biology·F H van BatenburgC W Pleij
Feb 2, 1999·Journal of Molecular Biology·E Rivas, S R Eddy
Dec 11, 1999·Nucleic Acids Research·F H van BatenburgJ Oliehoek
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·R B Lyngsø, C N Pedersen
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Jun 26, 2003·Nucleic Acids Research·Ivo L Hofacker
Aug 20, 2003·Journal of Computational Chemistry·Robert M Dirks, Niles A Pierce
Feb 26, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Samuel IeongSiu-Ming Yiu
Aug 12, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Einar Andreas Rødland
Oct 20, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Christina WitwerPeter F Stadler
Mar 27, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Baharak Rastegari, Anne Condon
Sep 22, 2007·Bulletin of Mathematical Biology·C Haslinger, P F Stadler
Mar 4, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hosna JabbariShelly Zhao

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Citations

Jul 14, 2012·PloS One·Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen

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Software Mentioned

IPeel
hspace
Mfold
STAR
Windows
HotKnots
Linux
FPack
OS X
Vienna

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