publication . Article . Other literature type . 2011

ViennaRNA Package 2.0

Christoph Flamm; Christian Höner zu Siederdissen; Hakim Tafer; Stephan H. Bernhart; Ronny Lorenz; Peter F. Stadler; Ivo L. Hofacker; Ivo L. Hofacker;
Open Access English
  • Published: 01 Nov 2011
Abstract
<p>Abstract</p> <p>Background</p> <p>Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties.</p> <p>Results</p> <p>The <monospace>ViennaRNA</monospace> Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Majo...
Subjects
free text keywords: ÖFOS 2002, Bioinformatik, ÖFOS 2002, Theoretische Chemie, KeyWords Plus: RNA SECONDARY STRUCTURE; BASE-PAIRING PROBABILITIES; DYNAMIC-PROGRAMMING ALGORITHM; CONTEXT-FREE GRAMMARS; STRUCTURE PREDICTION; EVOLUTIONARY OPTIMIZATION; THERMODYNAMIC PARAMETERS; AUTOMATIC DETECTION; PARTITION-FUNCTION; RIBONUCLEIC-ACIDS, ÖFOS 2002, Bioinformatics, ÖFOS 2002, Theoretical chemistry, KeyWords Plus: RNA SECONDARY STRUCTURE, BASE-PAIRING PROBABILITIES, DYNAMIC-PROGRAMMING ALGORITHM, CONTEXT-FREE GRAMMARS, STRUCTURE PREDICTION, EVOLUTIONARY OPTIMIZATION, THERMODYNAMIC PARAMETERS, AUTOMATIC DETECTION, PARTITION-FUNCTION, RIBONUCLEIC-ACIDS, Software Article, Biology (General), QH301-705.5, Genetics, QH426-470, Computational Theory and Mathematics, Applied Mathematics, Molecular Biology, Structural Biology, Rna secondary structure prediction, Consensus structure, Computer science, Minimum free energy, Partition function (statistical mechanics), Statistical physics, Intermediate level, Algorithm, Dynamic programming, Matthews correlation coefficient, Protein secondary structure
106 references, page 1 of 8

Thirumalai, D, Lee, N, Woodson, SA, Klimov, DK. Early Events in RNA Folding. Annu Rev Phys Chem. 2001; 52: 751-762 [OpenAIRE] [PubMed] [DOI]

Tinoco, I, Uhlenbeck, OC, Levine, MD. Estimation of Secondary Structure in Ribonucleic Acids. Nature. 1971; 230: 362-367 [OpenAIRE] [PubMed] [DOI]

Tinoco, I, Borer, PN, Dengler, B, Levine, ND, Uhlenbeck, OC, Crothers, DM, Gralla, J. Improved estimation of secondary structure in ribonucleic acids. Nature. 1973; 246: 40-41 [OpenAIRE]

Freier, SM, Kierzek, R, Jaeger, JA, Sugimoto, N, Caruthers, MH, Neilson, T, Turner, DH. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci, USA. 1986; 83: 9373-9377 [OpenAIRE] [PubMed] [DOI]

Jaeger, JA, Turner, DH, Zuker, M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci USA. 1989; 86: 7706-7710 [OpenAIRE] [PubMed] [DOI]

He, L, Kierzek, R, SantaLucia, J, Walter, AE, Turner, DH. Nearest-Neighbor Parameters for GU Mismatches. Biochemistry. 1991: 30 [OpenAIRE]

Xia, T, SanatLucia, J, Burkard, ME, Kierzek, R, Schroeder, SJ, Jiao, X, Cox, C, Turner, DH. Parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry. 1998; 37: 14719-14735 [OpenAIRE] [PubMed] [DOI]

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 (5): 911-940 [OpenAIRE] [PubMed] [DOI]

Mathews, DH, Disney, MD, Childs, JL, Schroeder, SJ, Zuker, M, Turner, DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction ofRNA secondary structure. Proc Natl Acad Sci USA. 2004; 101: 7287-7292 [OpenAIRE] [PubMed] [DOI]

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

Waterman, MS, Smith, TF. RNA secondary structure: A complete mathematical analysis. Mathematical Biosciences. 1978; 42: 257-266 [OpenAIRE] [DOI]

Nussinov, R, Jacobson, AB. Fast algorithm for predicting the secondary structure of single stranded RNA. Proc Natl Acad Sci USA. 1980; 77: 6309-6313 [OpenAIRE] [PubMed] [DOI]

Zuker, M, Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981; 9: 133-148 [OpenAIRE] [PubMed] [DOI]

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

McCaskill, JS. The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure. Biopolymers. 1990; 29: 1105-1119 [OpenAIRE] [PubMed] [DOI]

106 references, page 1 of 8
Related research
Abstract
<p>Abstract</p> <p>Background</p> <p>Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties.</p> <p>Results</p> <p>The <monospace>ViennaRNA</monospace> Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Majo...
Subjects
free text keywords: ÖFOS 2002, Bioinformatik, ÖFOS 2002, Theoretische Chemie, KeyWords Plus: RNA SECONDARY STRUCTURE; BASE-PAIRING PROBABILITIES; DYNAMIC-PROGRAMMING ALGORITHM; CONTEXT-FREE GRAMMARS; STRUCTURE PREDICTION; EVOLUTIONARY OPTIMIZATION; THERMODYNAMIC PARAMETERS; AUTOMATIC DETECTION; PARTITION-FUNCTION; RIBONUCLEIC-ACIDS, ÖFOS 2002, Bioinformatics, ÖFOS 2002, Theoretical chemistry, KeyWords Plus: RNA SECONDARY STRUCTURE, BASE-PAIRING PROBABILITIES, DYNAMIC-PROGRAMMING ALGORITHM, CONTEXT-FREE GRAMMARS, STRUCTURE PREDICTION, EVOLUTIONARY OPTIMIZATION, THERMODYNAMIC PARAMETERS, AUTOMATIC DETECTION, PARTITION-FUNCTION, RIBONUCLEIC-ACIDS, Software Article, Biology (General), QH301-705.5, Genetics, QH426-470, Computational Theory and Mathematics, Applied Mathematics, Molecular Biology, Structural Biology, Rna secondary structure prediction, Consensus structure, Computer science, Minimum free energy, Partition function (statistical mechanics), Statistical physics, Intermediate level, Algorithm, Dynamic programming, Matthews correlation coefficient, Protein secondary structure
106 references, page 1 of 8

Thirumalai, D, Lee, N, Woodson, SA, Klimov, DK. Early Events in RNA Folding. Annu Rev Phys Chem. 2001; 52: 751-762 [OpenAIRE] [PubMed] [DOI]

Tinoco, I, Uhlenbeck, OC, Levine, MD. Estimation of Secondary Structure in Ribonucleic Acids. Nature. 1971; 230: 362-367 [OpenAIRE] [PubMed] [DOI]

Tinoco, I, Borer, PN, Dengler, B, Levine, ND, Uhlenbeck, OC, Crothers, DM, Gralla, J. Improved estimation of secondary structure in ribonucleic acids. Nature. 1973; 246: 40-41 [OpenAIRE]

Freier, SM, Kierzek, R, Jaeger, JA, Sugimoto, N, Caruthers, MH, Neilson, T, Turner, DH. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci, USA. 1986; 83: 9373-9377 [OpenAIRE] [PubMed] [DOI]

Jaeger, JA, Turner, DH, Zuker, M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci USA. 1989; 86: 7706-7710 [OpenAIRE] [PubMed] [DOI]

He, L, Kierzek, R, SantaLucia, J, Walter, AE, Turner, DH. Nearest-Neighbor Parameters for GU Mismatches. Biochemistry. 1991: 30 [OpenAIRE]

Xia, T, SanatLucia, J, Burkard, ME, Kierzek, R, Schroeder, SJ, Jiao, X, Cox, C, Turner, DH. Parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry. 1998; 37: 14719-14735 [OpenAIRE] [PubMed] [DOI]

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 (5): 911-940 [OpenAIRE] [PubMed] [DOI]

Mathews, DH, Disney, MD, Childs, JL, Schroeder, SJ, Zuker, M, Turner, DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction ofRNA secondary structure. Proc Natl Acad Sci USA. 2004; 101: 7287-7292 [OpenAIRE] [PubMed] [DOI]

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

Waterman, MS, Smith, TF. RNA secondary structure: A complete mathematical analysis. Mathematical Biosciences. 1978; 42: 257-266 [OpenAIRE] [DOI]

Nussinov, R, Jacobson, AB. Fast algorithm for predicting the secondary structure of single stranded RNA. Proc Natl Acad Sci USA. 1980; 77: 6309-6313 [OpenAIRE] [PubMed] [DOI]

Zuker, M, Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981; 9: 133-148 [OpenAIRE] [PubMed] [DOI]

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

McCaskill, JS. The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure. Biopolymers. 1990; 29: 1105-1119 [OpenAIRE] [PubMed] [DOI]

106 references, page 1 of 8
Related research
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