Complete probabilistic analysis of RNA shapes

Voß B, Giegerich R, Rehmsmeier M (2006)
BMC Biology 4(1): 5.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Background: Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve reliable results. An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably. Folding space analysis comprises various methods such as suboptimal folding, computation of base pair probabilities, sampling procedures and abstract shape analysis. Common to many approaches is the idea of partitioning the folding space into classes of structures, for which certain properties can be derived. Results: In this paper we extend the approach of abstract shape analysis. We show how to compute the accumulated probabilities of all structures that share the same shape. While this implies a complete (non-heuristic) analysis of the folding space, the computational effort depends only on the size of the shape space, which is much smaller. This approach has been integrated into the tool RNAshapes, and we apply it to various RNAs. Conclusion: Analyses of conformational switches show the existence of two shapes with probabilities approximately 2/3 vs. 1/3, whereas the analysis of a microRNA precursor reveals one shape with a probability near to 1.0. Furthermore, it is shown that a shape can outperform an energetically more favourable one by achieving a higher probability. From these results, and the fact that we use a complete and exact analysis of the folding space, we conclude that this approach opens up new and promising routes for investigating and understanding RNA secondary structure.
BMC Biology
Page URI


Voß B, Giegerich R, Rehmsmeier M. Complete probabilistic analysis of RNA shapes. BMC Biology. 2006;4(1): 5.
Voß, B., Giegerich, R., & Rehmsmeier, M. (2006). Complete probabilistic analysis of RNA shapes. BMC Biology, 4(1), 5.
Voß, Björn, Giegerich, Robert, and Rehmsmeier, Marc. 2006. “Complete probabilistic analysis of RNA shapes”. BMC Biology 4 (1): 5.
Voß, B., Giegerich, R., and Rehmsmeier, M. (2006). Complete probabilistic analysis of RNA shapes. BMC Biology 4:5.
Voß, B., Giegerich, R., & Rehmsmeier, M., 2006. Complete probabilistic analysis of RNA shapes. BMC Biology, 4(1): 5.
B. Voß, R. Giegerich, and M. Rehmsmeier, “Complete probabilistic analysis of RNA shapes”, BMC Biology, vol. 4, 2006, : 5.
Voß, B., Giegerich, R., Rehmsmeier, M.: Complete probabilistic analysis of RNA shapes. BMC Biology. 4, : 5 (2006).
Voß, Björn, Giegerich, Robert, and Rehmsmeier, Marc. “Complete probabilistic analysis of RNA shapes”. BMC Biology 4.1 (2006): 5.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Access Level
OA Open Access
Zuletzt Hochgeladen
MD5 Prüfsumme

37 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Structural prediction of RNA switches using conditional base-pair probabilities.
Manzourolajdad A, Spouge JL., PLoS One 14(6), 2019
PMID: 31188853
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.
Boccaletto P, Magnus M, Almeida C, Zyla A, Astha A, Pluta R, Baginski B, Jankowska E, Dunin-Horkawicz S, Wirecki TK, Boniecki MJ, Stefaniak F, Bujnicki JM., Nucleic Acids Res 46(d1), 2018
PMID: 29069520
Compound image segmentation of published biomedical figures.
Li P, Jiang X, Kambhamettu C, Shatkay H., Bioinformatics 34(7), 2018
PMID: 29040394
Computational prediction of regulatory, premature transcription termination in bacteria.
Millman A, Dar D, Shamir M, Sorek R., Nucleic Acids Res 45(2), 2017
PMID: 27574119
The BRaliBase dent-a tale of benchmark design and interpretation.
Löwes B, Chauve C, Ponty Y, Giegerich R., Brief Bioinform 18(2), 2017
PMID: 26984616
Toward a next-generation atlas of RNA secondary structure.
Bai Y, Dai X, Harrison A, Johnston C, Chen M., Brief Bioinform 17(1), 2016
PMID: 25922372
New insights from cluster analysis methods for RNA secondary structure prediction.
Rogers E, Heitsch C., Wiley Interdiscip Rev RNA 7(3), 2016
PMID: 26971529
The RNA shapes studio.
Janssen S, Giegerich R., Bioinformatics 31(3), 2015
PMID: 25273103
Pareto optimization in algebraic dynamic programming.
Saule C, Giegerich R., Algorithms Mol Biol 10(), 2015
PMID: 26150892
Algebraic Dynamic Programming over general data structures.
zu Siederdissen CH, Prohaska SJ, Stadler PF., BMC Bioinformatics 16 Suppl 19(), 2015
PMID: 26695390
Combinatorics of locally optimal RNA secondary structures.
Fusy E, Clote P., J Math Biol 68(1-2), 2014
PMID: 23263300
Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble.
Rogers E, Heitsch CE., Nucleic Acids Res 42(22), 2014
PMID: 25392423
Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.
Achawanantakun R, Sun Y., BMC Bioinformatics 14 Suppl 2(), 2013
PMID: 23369147
A silent exonic SNP in kdm3a affects nucleic acids structure but does not regulate experimental autoimmune encephalomyelitis.
Gillett A, Bergman P, Parsa R, Bremges A, Giegerich R, Jagodic M., PLoS One 8(12), 2013
PMID: 24312603
Topology of RNA-RNA interaction structures.
Andersen JE, Huang FW, Penner RC, Reidys CM., J Comput Biol 19(7), 2012
PMID: 22731621
Topology and prediction of RNA pseudoknots.
Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME., Bioinformatics 27(8), 2011
PMID: 21335320
Semantics and ambiguity of stochastic RNA family models.
Giegerich R, Höner zu Siederdissen C., IEEE/ACM Trans Comput Biol Bioinform 8(2), 2011
PMID: 21233528
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.
Janssen S, Schudoma C, Steger G, Giegerich R., BMC Bioinformatics 12(), 2011
PMID: 22051375
Faster computation of exact RNA shape probabilities.
Janssen S, Giegerich R., Bioinformatics 26(5), 2010
PMID: 20080511
Computational generation and screening of RNA motifs in large nucleotide sequence pools.
Kim N, Izzo JA, Elmetwaly S, Gan HH, Schlick T., Nucleic Acids Res 38(13), 2010
PMID: 20448026
Computational approaches to 3D modeling of RNA.
Laing C, Schlick T., J Phys Condens Matter 22(28), 2010
PMID: 21399271
Folding and finding RNA secondary structure.
Mathews DH, Moss WN, Turner DH., Cold Spring Harb Perspect Biol 2(12), 2010
PMID: 20685845
Shapes of RNA pseudoknot structures.
Reidys CM, Wang RR., J Comput Biol 17(11), 2010
PMID: 20868269
Strategies for measuring evolutionary conservation of RNA secondary structures.
Gruber AR, Bernhart SH, Hofacker IL, Washietl S., BMC Bioinformatics 9(), 2008
PMID: 18302738
Shape based indexing for faster search of RNA family databases.
Janssen S, Reeder J, Giegerich R., BMC Bioinformatics 9(), 2008
PMID: 18312625
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.
Liu Q, Yang Y, Chen C, Bu J, Zhang Y, Ye X., BMC Bioinformatics 9(), 2008
PMID: 18373878
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
Liu Q, Olman V, Liu H, Ye X, Qiu S, Xu Y., J Comput Chem 29(9), 2008
PMID: 18271070
Bridging the gap in RNA structure prediction.
Shapiro BA, Yingling YG, Kasprzak W, Bindewald E., Curr Opin Struct Biol 17(2), 2007
PMID: 17383172
RNAbor: a web server for RNA structural neighbors.
Freyhult E, Moulton V, Clote P., Nucleic Acids Res 35(web server issue), 2007
PMID: 17526527
Boltzmann probability of RNA structural neighbors and riboswitch detection.
Freyhult E, Moulton V, Clote P., Bioinformatics 23(16), 2007
PMID: 17573364
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions.
Hiller M, Pudimat R, Busch A, Backofen R., Nucleic Acids Res 34(17), 2006
PMID: 16987907
Structural analysis of aligned RNAs.
Voss B., Nucleic Acids Res 34(19), 2006
PMID: 17020924

33 References

Daten bereitgestellt von Europe PubMed Central.

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Mathews DH, Sabina J, Zuker M, Turner DH., J. Mol. Biol. 288(5), 1999
PMID: 10329189
A statistical sampling algorithm for RNA secondary structure prediction.
Ding Y, Lawrence CE., Nucleic Acids Res. 31(24), 2003
PMID: 14654704
Co-transcriptional folding is encoded within RNA genes.
Meyer IM, Miklos I., BMC Mol. Biol. 5(), 2004
PMID: 15298702
On finding all suboptimal foldings of an RNA molecule.
Zuker M., Science 244(4900), 1989
PMID: 2468181
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
Zuker M, Mathews D, Turner D., 1999
Complete suboptimal folding of RNA and the stability of secondary structures.
Wuchty S, Fontana W, Hofacker IL, Schuster P., Biopolymers 49(2), 1999
PMID: 10070264
Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package)
Hofacker I, Fontana W, Stadler P, Bonhoeffer L, Tacker M, Schuster P., 1994
Identification of common molecular subsequences.
Smith TF, Waterman MS., J. Mol. Biol. 147(1), 1981
PMID: 7265238
Prediction and visualization of structural switches in RNA.
Giegerich R, Haase D, Rehmsmeier M., Pac Symp Biocomput (), 1999
PMID: 10380191
Evaluating the predictability of conformational switching in RNA.
Voss B, Meyer C, Giegerich R., Bioinformatics 20(10), 2004
PMID: 14962925
Barrier Trees of Degenerate Landscapes
Flamm C, Hofacker I, Stadler P, Wolfinger M., 2002
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
Explaining and Controlling Ambiguity in Dynamic Programming
Giegerich R., 2000
Effective ambiguity checking in biosequence analysis.
Reeder J, Steffen P, Giegerich R., BMC Bioinformatics 6(), 2005
PMID: 15967024
A Discipline of Dynamic Programming over Sequence Data
Giegerich R, Meyer C, Steffen P., 2004
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
Walter AE, Turner DH, Kim J, Lyttle MH, Muller P, Mathews DH, Zuker M., Proc. Natl. Acad. Sci. U.S.A. 91(20), 1994
PMID: 7524072
Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops.
Chen G, Znosko BM, Jiao X, Turner DH., Biochemistry 43(40), 2004
PMID: 15461459

Le S, Chen J, Maizel J., 1990
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.
Clote P, Ferre F, Kranakis E, Krizanc D., RNA 11(5), 2005
PMID: 15840812

Bellmann R., 1957
RNAshapes: an integrated RNA analysis package based on abstract shapes.
Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R., Bioinformatics 22(4), 2005
PMID: 16357029

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

PMID: 16480488
PubMed | Europe PMC

Suchen in

Google Scholar