Random generation of RNA secondary structures according to native distributions

Nebel M, Scheid A, Weinberg F (2011)
Algorithms for Molecular Biology 6(1): 24.

Zeitschriftenaufsatz | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Nebel, MarkusUniBi; Scheid, Anika; Weinberg, Frank
Erscheinungsjahr
2011
Zeitschriftentitel
Algorithms for Molecular Biology
Band
6
Ausgabe
1
Art.-Nr.
24
ISSN
1748-7188
Page URI
https://pub.uni-bielefeld.de/record/2910017

Zitieren

Nebel M, Scheid A, Weinberg F. Random generation of RNA secondary structures according to native distributions. Algorithms for Molecular Biology. 2011;6(1): 24.
Nebel, M., Scheid, A., & Weinberg, F. (2011). Random generation of RNA secondary structures according to native distributions. Algorithms for Molecular Biology, 6(1), 24. doi:10.1186/1748-7188-6-24
Nebel, Markus, Scheid, Anika, and Weinberg, Frank. 2011. “Random generation of RNA secondary structures according to native distributions”. Algorithms for Molecular Biology 6 (1): 24.
Nebel, M., Scheid, A., and Weinberg, F. (2011). Random generation of RNA secondary structures according to native distributions. Algorithms for Molecular Biology 6:24.
Nebel, M., Scheid, A., & Weinberg, F., 2011. Random generation of RNA secondary structures according to native distributions. Algorithms for Molecular Biology, 6(1): 24.
M. Nebel, A. Scheid, and F. Weinberg, “Random generation of RNA secondary structures according to native distributions”, Algorithms for Molecular Biology, vol. 6, 2011, : 24.
Nebel, M., Scheid, A., Weinberg, F.: Random generation of RNA secondary structures according to native distributions. Algorithms for Molecular Biology. 6, : 24 (2011).
Nebel, Markus, Scheid, Anika, and Weinberg, Frank. “Random generation of RNA secondary structures according to native distributions”. Algorithms for Molecular Biology 6.1 (2011): 24.

2 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

An Efficient Dual Sampling Algorithm with Hamming Distance Filtration.
Barrett C, He Q, Huang FW, Reidys CM., J Comput Biol 25(11), 2018
PMID: 30133328
Analysis of the free energy in a stochastic RNA secondary structure model.
Nebel ME, Scheid A., IEEE/ACM Trans Comput Biol Bioinform 8(6), 2011
PMID: 21116040

49 References

Daten bereitgestellt von Europe PubMed Central.

Boltzmann Sampling of Unlabelled Structures
AUTHOR UNKNOWN, 2007
Random sequences.
Fitch WM., J. Mol. Biol. 163(2), 1983
PMID: 6842586
Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage
AUTHOR UNKNOWN, 1985
Random Generation of structured genomic sequences
AUTHOR UNKNOWN, 2003
Secondary Structure of Single-Stranded Nucleic Acids
AUTHOR UNKNOWN, 1978
A statistical sampling algorithm for RNA secondary structure prediction.
Ding Y, Lawrence CE., Nucleic Acids Res. 31(24), 2003
PMID: 14654704
Benchmarking RNA secondary structures comparison algorithms
AUTHOR UNKNOWN, 2008
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
On finding all suboptimal foldings of an RNA molecule.
Zuker M., Science 244(4900), 1989
PMID: 2468181
Vienna RNA secondary structure server.
Hofacker IL., Nucleic Acids Res. 31(13), 2003
PMID: 12824340
Pfold: RNA secondary structure prediction using stochastic context-free grammars.
Knudsen B, Hein J., Nucleic Acids Res. 31(13), 2003
PMID: 12824339
A comparative method for finding and folding RNA secondary structures within protein-coding regions.
Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J., Nucleic Acids Res. 32(16), 2004
PMID: 15448187
An evolutionary model for protein-coding regions with conserved RNA structure.
Pedersen JS, Forsberg R, Meyer IM, Hein J., Mol. Biol. Evol. 21(10), 2004
PMID: 15229291
In silico sequence evolution with site-specific interactions along phylogenetic trees.
Gesell T, von Haeseler A., Bioinformatics 22(6), 2005
PMID: 16332711

AUTHOR UNKNOWN, 2010
Analysis of the Free Energy in a Stochastic RNA Secondary Structure Model
AUTHOR UNKNOWN, 2010
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.
Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH., Biochemistry 37(42), 1998
PMID: 9778347
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

AUTHOR UNKNOWN, 1978
A Calculus for the Random Generation of Combinatorial Structures
AUTHOR UNKNOWN, 1994
Boltzmann Samplers for the Random Generation of Combinatorial Structures
AUTHOR UNKNOWN, 2004

AUTHOR UNKNOWN, 2009

AUTHOR UNKNOWN, 1978
On some new sequences generalizing the Catalan and Motzkin numbers
AUTHOR UNKNOWN, 1978
Enumeration of RNA Secondary Structures by Complexity
AUTHOR UNKNOWN, 1985
Combinatorial properties of RNA secondary structures.
Nebel ME., J. Comput. Biol. 9(3), 2002
PMID: 12162892
Combinatorics of RNA secondary structures
AUTHOR UNKNOWN, 1998
Investigation of the Bernoulli model for RNA secondary structures.
Nebel ME., Bull. Math. Biol. 66(5), 2004
PMID: 15294413
RNA Secondary Structures and their Prediction
AUTHOR UNKNOWN, 1984

AUTHOR UNKNOWN, 2002
Identifying Good Predictions of RNA Secondary Structure
AUTHOR UNKNOWN, 2004
Ordered Generation of Classes of Combinatorial Structures
AUTHOR UNKNOWN, 2005
Stochastic Grammars and Languages
AUTHOR UNKNOWN, 1972
On Stochastic Context-Free Languages
AUTHOR UNKNOWN, 1971
Stochastic context-free grammars for tRNA modeling.
Sakakibara Y, Brown M, Hughey R, Mian IS, Sjolander K, Underwood RC, Haussler D., Nucleic Acids Res. 22(23), 1994
PMID: 7800507
Ranking and unranking of lexicographically ordered words: an average-case analysis
AUTHOR UNKNOWN, 1998
Extending Stochastic Context-Free Grammars for an Application in Bioin-formatics
AUTHOR UNKNOWN, 2010
Query-dependent banding (QDB) for faster RNA similarity searches.
Nawrocki EP, Eddy SR., PLoS Comput. Biol. 3(3), 2007
PMID: 17397253
A generic approach for the unranking of labeled combinatorial classes. Random Struct
AUTHOR UNKNOWN, 2001
The European Large Subunit Ribosomal RNA Database.
Wuyts J, De Rijk P, Van de Peer Y, Winkelmans T, De Wachter R., Nucleic Acids Res. 29(1), 2001
PMID: 11125083
The European database on small subunit ribosomal RNA.
Wuyts J, Van de Peer Y, Winkelmans T, De Wachter R., Nucleic Acids Res. 30(1), 2002
PMID: 11752288

AUTHOR UNKNOWN, 1978
On a test of whether one of two random variables is stochastically larger than the other
AUTHOR UNKNOWN, 1947
Individual Comparisons by Ranking Methods
AUTHOR UNKNOWN, 1945
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 21992500
PubMed | Europe PMC

Suchen in

Google Scholar