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2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
July-Aug. 2013 (vol. 10 no. 4)
pp. 832-844
Ronny Lorenz, Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Stephan H. Bernhart, Dept. of Comput. Sci., Univ. of Leipzig, Leipzig, Germany
Jing Qin, Max Planck Inst. for Math. in the Sci., Leipzig, Germany
Christian Honer Zu Siederdissen, Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Andrea Tanzer, Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Fabian Amman, Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Ivo L. Hofacker, Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Peter F. Stadler, Dept. of Comput. Sci., Univ. of Leipzig, Leipzig, Germany
G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters, we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead. Stable G-quadruplexes are strongly enriched, however, in the 5Ê1UTR of protein coding mRNAs.
Index Terms:
RNA,dynamic programming,genomics,molecular biophysics,molecular configurations,proteins,protein coding mRNA,G-quadruplexes,RNA secondary structure prediction,locally stable structural elements,nucleic acids,combinatorial theory,dynamic programming algorithms,plausible energy model,energy parameters,putative quadruplex-forming sequences,human genome,canonical secondary structures,RNA,Shape,Bioinformatics,Temperature measurement,Computational biology,Humans,DNA,HASH(0x4eb4c2c)
Citation:
Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Honer Zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler, "2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 4, pp. 832-844, July-Aug. 2013, doi:10.1109/TCBB.2013.7
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