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Topological classification of RNA structures [article]

Michael Bon, Graziano Vernizzi, Henri Orland, A. Zee
2006 arXiv   pre-print
We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure.  ...  In such a representation, planar diagrams correspond to pure RNA secondary structures and have zero genus, whereas non planar diagrams correspond to pseudoknotted structures and have higher genus.  ...  Such a primitive structure is decorated by 6 additional simple pseudoknots of type H and K (type a) and b) in the first column of fig.6 , respectively). c Figure 12 : The B chain of PDB 1vp0 is an RNA  ... 
arXiv:q-bio/0607032v1 fatcat:4vo62b5yhjhzbbxipjdoqapqlu

A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots

Xiang Chen, Si-Min He, Dong-Bo Bu, Run-Sheng Chen, Wen Gao
2007 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering  
We demonstrate a new algorithm named FlexStem to predict RNA secondary structures with pseudoknots.  ...  Our approach is based on the free energy minimization criterion, and utilizes a sophisticated energy model that is more accurate and supports more types of pseudoknots.  ...  This work was supported by the National Key Basic R&D Program (973) of China (2002CB713807) and the CAS Knowledge Innovation Program (20076020).  ... 
doi:10.1109/bibe.2007.4375595 dblp:conf/bibe/ChenHBCG07 fatcat:6qu3b6svjzarrfpgpsfhxwb2du

Asymmetry in RNA pseudoknots: observation and theory

D. P. Aalberts
2005 Nucleic Acids Research  
Our examination of the PseudoBase database of pseudoknotted RNA structures reveals asymmetries in the stem and loop lengths and provocative composition differences between the loops.  ...  By taking into account differences between major and minor grooves of the RNA double helix, we explain much of the asymmetry with a simple polymer physics model and statistical mechanical theory, with  ...  ACKNOWLEDGEMENTS The authors thank Jesse Dill for noticing the duplications in PseudoBase and assisting with Table 1 . This work was supported by National Institutes of Health grant GM068485.  ... 
doi:10.1093/nar/gki508 pmid:15831794 pmcid:PMC1079967 fatcat:xypzglxl7fh25dfhfuaywgpm54

K-Partite RNA Secondary Structures [chapter]

Minghui Jiang, Pedro J. Tejada, Ramoni O. Lasisi, Shanhong Cheng, D. Scott Fechser
2009 Lecture Notes in Computer Science  
Experiment on sequences from PseudoBase shows that our first-fit packing heuristic outperforms the leading method HotKnots in predicting RNA secondary structures with pseudoknots.  ...  We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots.  ...  During the last decade, several dynamic programming algorithms have also been designed for the much more difficult problem of predicting RNA secondary structures with pseudoknots [24, 27, 19, 2, 8, 22  ... 
doi:10.1007/978-3-642-04241-6_14 fatcat:zrhwuirm75bndexzmu2egkixoa

compPknots: A Framework for Parallel Prediction and Comparison of RNA Secondary Structures with Pseudoknots [chapter]

Trilce Estrada, Abel Licon, Michela Taufer
2006 Lecture Notes in Computer Science  
Codes for RNA structure prediction based on energy minimization are usually very time and resource intensive.  ...  structures with reduced lengths, or they are only able to predict some elementary and simple pseudoknots.  ...  Acknowledgments This material is based in part upon work supported by the Texas Advanced Research Program under Grant No. 003661-0008-2006.  ... 
doi:10.1007/11942634_70 fatcat:wz66xhfcmvfejdopm2jkijf45q

Pseudoknots in RNA folding landscapes

Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin
2015 Bioinformatics  
We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures.  ...  Results We generalize the basin hopping graph framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted  ...  This class comprises the four basic types of pseudoknots shown in Fig. 1 -the most common H-type and kissing hairpin (K-type) together with more exotic L-type and M-type pseudoknots.  ... 
doi:10.1093/bioinformatics/btv572 pmid:26428288 pmcid:PMC4708108 fatcat:awoxayhfvbenfb6lfptdygrvj4

Soft Computing based Model for Identification of Pseudoknots in RNA Sequence using Learning Grammar

Ankita Jiwan, Shailendra Singh
2012 International Journal of Computer Applications  
RNA structure prediction is one of the major topics in bioinformatics. Among the various RNA structures, pseudoknots are the most complex and unique structure.  ...  Various methods have been used for modeling RNA pseudoknotted secondary structure. In this paper a new model for prediction of RNA pseudoknot structure has been proposed.  ...  RNA Pseudoknot Structure Prediction Techniques The following techniques exist to predict the structure of RNA pseudoknots: Dynamic programming Dynamic programming is a very well known and usefull method  ... 
doi:10.5120/8591-2344 fatcat:gixwe3id6fgyxorpr2ztbu2o44

Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design

H. H. Gan
2003 Nucleic Acids Research  
To expand known RNA structural motifs, we develop a two-dimensional graphical representation approach for describing and estimating the size of RNA's secondary structural repertoire, including naturally  ...  We employ tree graphs to describe RNA tree motifs and more general (dual) graphs to describe both RNA tree and pseudoknot motifs.  ...  Patel and Eric Westhof for constructive comments on aspects of this work.  ... 
doi:10.1093/nar/gkg365 pmid:12771219 pmcid:PMC156709 fatcat:otds6qix2rbodnjtmiama37fwy

pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows

J. Reeder, P. Steffen, R. Giegerich
2007 Nucleic Acids Research  
ACKNOWLEDGEMENTS We thank Jan Kru¨ger for the Web Service implementation of pknotsRG and for the initial connection to the PseudoViewer Web Service.  ...  If the loop regions u, v, w fold further internal structures, including pseudoknots of this type, we have a simple recursive pseudoknot.  ...  CHARACTERIZATION OF THE RECOGNIZED CLASS OF PSEUDOKNOTS General pseudoknot prediction in energy-based models is a Non-deterministic Polynomial time NP-complete problem (14) , and thus requires exponential  ... 
doi:10.1093/nar/gkm258 pmid:17478505 pmcid:PMC1933184 fatcat:46zpo4hmqjg5dhji5saadhdzry

Classifying RNA pseudoknotted structures

Anne Condon, Beth Davy, Baharak Rastegari, Shelly Zhao, Finbarr Tarrant
2004 Theoretical Computer Science  
Computational prediction of the minimum free energy (mfe) secondary structure of an RNA molecule from its base sequence is valuable in understanding the structure and function of the molecule.  ...  We report on the percentage of biological structures from the PseudoBase and Gutell databases that are handled by these two algorithms.  ...  Acknowledgements We thank Mirela Andronescu, Matthew Cook, Robert Dirks, Holger Hoos, Niles Pierce, Joseph Schaeffer, Dan Tulpan, and Erik Winfree for valuable feedback on earlier versions of this work  ... 
doi:10.1016/j.tcs.2004.03.042 fatcat:3v33od3s6vh6tjp3bnxix6n244

Classifying RNA pseudoknotted structures

A CONDON
2004 Theoretical Computer Science  
Computational prediction of the minimum free energy (mfe) secondary structure of an RNA molecule from its base sequence is valuable in understanding the structure and function of the molecule.  ...  We report on the percentage of biological structures from the PseudoBase and Gutell databases that are handled by these two algorithms.  ...  Acknowledgements We thank Mirela Andronescu, Matthew Cook, Robert Dirks, Holger Hoos, Niles Pierce, Joseph Schaeffer, Dan Tulpan, and Erik Winfree for valuable feedback on earlier versions of this work  ... 
doi:10.1016/s0304-3975(04)00193-8 fatcat:si3linfp35fp5jvw4e7o3xgwri

Topology and prediction of RNA pseudoknots

Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel
2011 Computer applications in the biosciences : CABIOS  
Motivation: Several dynamic programming algorithms for predicting RNA structures with pseudoknots have been proposed that differ dramatically from one another in the classes of structures considered.  ...  It admits a topology-dependent parametrization of pseudoknot penalties that increases the sensitivity and positive predictive value of predicted base pairs by 10-20% compared with earlier approaches.  ...  Although the vast majority of RNAs has simple, * To whom correspondence should be addressed. i.e. pseudoknot-free, secondary structure, PseudoBase (Taufer et al., 2009) lists more than 250 records of  ... 
doi:10.1093/bioinformatics/btr090 pmid:21335320 fatcat:6aj7j2e4wfbvrm7zm6rvznwtoa

On the page number of RNA secondary structures with pseudoknots

Peter Clote, Stefan Dobrev, Ivan Dotu, Evangelos Kranakis, Danny Krizanc, Jorge Urrutia
2011 Journal of Mathematical Biology  
Let S denote the set of (possibly noncanonical) base pairs {i, j} of an RNA tertiary structure; i.e. {i, j} ∈ S if there is a hydrogen bond between the ith and jth nucleotide.  ...  Here, we show that computing the page number is NP-complete; we describe an exact computation of page number, using constraint programming, and determine the page number of a collection of RNA tertiary  ...  Clote and I. Dotu was provided by the National Science Foundation with grants DMS-1016618 and DMS-0817971, with additional funding to P.C. by Digiteo Foundation.  ... 
doi:10.1007/s00285-011-0493-6 pmid:22159642 fatcat:c5dpvjcxafep5fbpatoesiwogm

A graphical criterion of planarity for RNA secondary structures with pseudoknots in Rivas–Eddy class

Shile Gao, Kequan Ding
2008 Theoretical Computer Science  
In this paper, a graphical criterion of planarity is presented based on graphical composition for RNA secondary structures with pseudoknots in Rivas-Eddy Class.  ...  An RNA secondary structure is considered to be planar if its arc graph can be embedded into a plane without edge crossing.  ...  Rivas and Eddy [7, 8] have proposed a dynamic programming algorithm, R&E algorithm, for RNA secondary structure prediction including pseudoknots.  ... 
doi:10.1016/j.tcs.2007.09.026 fatcat:h2iuy4te2jffvgytcb5vd4gwiq

Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications

Markus E. Nebel, Frank Weinberg
2012 Journal of Computational Biology  
Predicting RNA structures with pseudoknots in generell is an NP-complete problem.  ...  Accordingly, several authors have suggested subclasses which provide polynomial time prediction algorithms by allowing resp. disallowing certain structural motives.  ...  Even though the vast majority of RNAs has simple, i.e., pseudoknot-free, secondary structure, PseudoBase [27] lists more than 300 records of pseudoknots determined by a variety of experimental and computational  ... 
doi:10.1089/cmb.2011.0094 pmid:23057823 pmcid:PMC3469209 fatcat:ufztylaeavbmvgh3oxucbqre5y
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