publication . Article . 2013

The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective.

Elena Rivas;
Open Access
  • Published: 01 May 2013 Journal: RNA Biology, volume 10, pages 1,185-1,196 (issn: 1547-6286, eissn: 1555-8584, Copyright policy)
  • Publisher: Informa UK Limited
Abstract
Any method for RNA secondary structure prediction is determined by four ingredients. The architecture is the choice of features implemented by the model (such as stacked basepairs, loop length distributions, etc.). The architecture determines the number of parameters in the model. The scoring scheme is the nature of those parameters (whether thermodynamic, probabilistic, or weights). The parameterization stands for the specific values assigned to the parameters. These three ingredients are referred to as “the model.” The fourth ingredient is the folding algorithms used to predict plausible secondary structures given the model and the sequence of a structural RNA...
Subjects
free text keywords: Cell Biology, Molecular Biology, Research Paper, context-free grammars, thermodynamic parameters, probabilistic models, statistical training, RNA, Probabilistic logic, Rna secondary structure prediction, Single sequence, Context-free grammar, Bioinformatics, Parametrization, Software, business.industry, business, Algorithm, Biology, Ceiling (aeronautics)
99 references, page 1 of 7

Nussinov, R, Pieczenik, G, Griggs, JR, Kleitman, DJ. Algorithms for loop matchings. SIAM J Appl Math. 1978; 35: 68-82 [OpenAIRE] [DOI]

Waterman, MS, Smith, TF. RNA secondary structure: A complete mathematical analysis. Math Biosci. 1978; 42: 257-66 [OpenAIRE] [DOI]

Zuker, M, Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981; 9: 133-48 [OpenAIRE] [PubMed] [DOI]

Zuker, M, Sankoff, S. RNA secondary structures and their prediction. Bull Math Biol. 1984; 46: 591-621 [OpenAIRE]

Tinoco, I, Uhlenbeck, OC, Levine, MD. Estimation of secondary structure in ribonucleic acids. Nature. 1971; 230: 362-7 [OpenAIRE] [PubMed] [DOI]

Freier, SM, Kierzek, R, Jaeger, JA, Sugimoto, N, Caruthers, MH, Neilson, T. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA. 1986; 83: 9373-7 [OpenAIRE] [PubMed] [DOI]

Turner, DH, Sugimoto, N, Jaeger, JA, Longfellow, CE, Freier, SM, Kierzek, R. Improved parameters for prediction of RNA structure. Cold Spring Harb Symp Quant Biol. 1987; 52: 123-33 [OpenAIRE] [PubMed] [DOI]

Kim, J, Walter, AE, Turner, DH. Thermodynamics of coaxially stacked helixes with GA and CC mismatches. Biochemistry. 1996; 35: 13753-61 [OpenAIRE] [PubMed] [DOI]

Xia, T, Jr SantaLucia, J, Burkard, ME, Kierzek, R, Schroeder, SJ. X. Jiao anc C. Cox, and D. H. Turner. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemestry. 1998; 37: 14719-35 [OpenAIRE] [DOI]

10 Mathews DH, Andre TC, Kim J, Turner DH, Zuker M. An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters. In N. B. Leontis and J. Jr Santalucia, editors, Molecular Modeling of Nucleic Acids, pages 246–257. American Chemical Society, 1998.

Mathews, DH, Sabina, J, Zuker, M, Turner, DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 1999; 288: 911-40 [OpenAIRE] [PubMed] [DOI]

Liu, B, Diamond, JM, Mathews, DH, Turner, DH. Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters. Biochemistry. 2011; 50: 640-53 [OpenAIRE] [PubMed] [DOI]

Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31: 3406-15 [OpenAIRE] [PubMed] [DOI]

14 Markham NR, Zuker M. UNAFold: software for nucleic acid folding and hybriziation. In J. M. Keith, editor, Bioinformatics, Volume II. Structure, Function and Applications, chapter 1, pages 3–31. Humana Press, Totowa, NJ, 2008.

Hofacker, IL, Fontana, W, Stadler, PF, Bonhoeffer, LS, Tacker, M, Schuster, P. Fast folding and comparison of RNA secondary structures (the Vienna RNA package). Monatsh Chem. 1994; 125: 167-88 [DOI]

99 references, page 1 of 7
Abstract
Any method for RNA secondary structure prediction is determined by four ingredients. The architecture is the choice of features implemented by the model (such as stacked basepairs, loop length distributions, etc.). The architecture determines the number of parameters in the model. The scoring scheme is the nature of those parameters (whether thermodynamic, probabilistic, or weights). The parameterization stands for the specific values assigned to the parameters. These three ingredients are referred to as “the model.” The fourth ingredient is the folding algorithms used to predict plausible secondary structures given the model and the sequence of a structural RNA...
Subjects
free text keywords: Cell Biology, Molecular Biology, Research Paper, context-free grammars, thermodynamic parameters, probabilistic models, statistical training, RNA, Probabilistic logic, Rna secondary structure prediction, Single sequence, Context-free grammar, Bioinformatics, Parametrization, Software, business.industry, business, Algorithm, Biology, Ceiling (aeronautics)
99 references, page 1 of 7

Nussinov, R, Pieczenik, G, Griggs, JR, Kleitman, DJ. Algorithms for loop matchings. SIAM J Appl Math. 1978; 35: 68-82 [OpenAIRE] [DOI]

Waterman, MS, Smith, TF. RNA secondary structure: A complete mathematical analysis. Math Biosci. 1978; 42: 257-66 [OpenAIRE] [DOI]

Zuker, M, Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981; 9: 133-48 [OpenAIRE] [PubMed] [DOI]

Zuker, M, Sankoff, S. RNA secondary structures and their prediction. Bull Math Biol. 1984; 46: 591-621 [OpenAIRE]

Tinoco, I, Uhlenbeck, OC, Levine, MD. Estimation of secondary structure in ribonucleic acids. Nature. 1971; 230: 362-7 [OpenAIRE] [PubMed] [DOI]

Freier, SM, Kierzek, R, Jaeger, JA, Sugimoto, N, Caruthers, MH, Neilson, T. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA. 1986; 83: 9373-7 [OpenAIRE] [PubMed] [DOI]

Turner, DH, Sugimoto, N, Jaeger, JA, Longfellow, CE, Freier, SM, Kierzek, R. Improved parameters for prediction of RNA structure. Cold Spring Harb Symp Quant Biol. 1987; 52: 123-33 [OpenAIRE] [PubMed] [DOI]

Kim, J, Walter, AE, Turner, DH. Thermodynamics of coaxially stacked helixes with GA and CC mismatches. Biochemistry. 1996; 35: 13753-61 [OpenAIRE] [PubMed] [DOI]

Xia, T, Jr SantaLucia, J, Burkard, ME, Kierzek, R, Schroeder, SJ. X. Jiao anc C. Cox, and D. H. Turner. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemestry. 1998; 37: 14719-35 [OpenAIRE] [DOI]

10 Mathews DH, Andre TC, Kim J, Turner DH, Zuker M. An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters. In N. B. Leontis and J. Jr Santalucia, editors, Molecular Modeling of Nucleic Acids, pages 246–257. American Chemical Society, 1998.

Mathews, DH, Sabina, J, Zuker, M, Turner, DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 1999; 288: 911-40 [OpenAIRE] [PubMed] [DOI]

Liu, B, Diamond, JM, Mathews, DH, Turner, DH. Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters. Biochemistry. 2011; 50: 640-53 [OpenAIRE] [PubMed] [DOI]

Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31: 3406-15 [OpenAIRE] [PubMed] [DOI]

14 Markham NR, Zuker M. UNAFold: software for nucleic acid folding and hybriziation. In J. M. Keith, editor, Bioinformatics, Volume II. Structure, Function and Applications, chapter 1, pages 3–31. Humana Press, Totowa, NJ, 2008.

Hofacker, IL, Fontana, W, Stadler, PF, Bonhoeffer, LS, Tacker, M, Schuster, P. Fast folding and comparison of RNA secondary structures (the Vienna RNA package). Monatsh Chem. 1994; 125: 167-88 [DOI]

99 references, page 1 of 7
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