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2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
PrePrint
ISSN: 1545-5963
ASCII Text
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Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Honer zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, "2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 99, no. 1, pp. 1, , 5555.
 
 
BibTex
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@article{ 10.1109/TCBB.2013.7,
author = {Ronny Lorenz and Stephan H. Bernhart and Jing Qin and Christian Honer zu Siederdissen and Andrea Tanzer and Fabian Amman and Ivo L. Hofacker},
title = {2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {99},
number = {1},
issn = {1545-5963},
year = {5555},
pages = {1},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.7},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
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TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - 2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
IS - 1
SN - 1545-5963
SP
EP
EPD - 1
A1 - Ronny Lorenz,
A1 - Stephan H. Bernhart,
A1 - Jing Qin,
A1 - Christian Honer zu Siederdissen,
A1 - Andrea Tanzer,
A1 - Fabian Amman,
A1 - Ivo L. Hofacker,
PY - 5555
KW - Biology and genetics
KW - Mathematics of Computing
KW - Discrete Mathematics
KW - Combinatorics
KW - Counting problems
KW - Graph Theory
KW - Graph algorithms
KW - Applications
KW - Computing Methodologies
KW - Artificial Intelligence
KW - Problem Solving
KW - Control Methods
KW - and Search
KW - Dynamic programming
KW - Computer Applications
KW - Life and Medical Sciences
VL - 99
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Ronny Lorenz, University of Vienna, Vienna
Stephan H. Bernhart, University of Leipzig, Leipzig
Jing Qin, Max Planck Institute for Mathematics in the Sciences, Leipzig and University of Leipzig, Leipzig
Christian Honer zu Siederdissen, University of Vienna, Vienna
Andrea Tanzer, University of Vienna, Vienna and Center for Genomic Regulation (CRG), Barcelona
Fabian Amman, University of Vienna, Vienna
Ivo L. Hofacker, University of Vienna, Vienna and University of Copenhagen
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 5' UTR of protein coding mRNAs.
Index Terms:
Biology and genetics,Mathematics of Computing,Discrete Mathematics,Combinatorics,Counting problems,Graph Theory,Graph algorithms,Applications,Computing Methodologies,Artificial Intelligence,Problem Solving,Control Methods,and Search,Dynamic programming,Computer Applications,Life and Medical Sciences
Citation:
Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Honer zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, "2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 24 Jan. 2013. IEEE computer Society Digital Library. IEEE Computer Society, <http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.7>
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