Abstract
The effect of more detailed modeling of the interface between stem and loop in non-coding RNA hairpin structures on efficacy of covariance-model-based non-coding RNA gene search is examined. Currently, the prior probabilities of the two stem nucleotides and two loop-end nucleotides at the interface are treated the same as any other stem and loop nucleotides respectively. Laboratory thermodynamic studies show that hairpin stability is dependent on the identities of these four nucleotides, but this is not taken into account in current covariance models. It is shown that separate estimation of emission priors for these nucleotides and joint treatment of substitution probabilities for the two loop-end nucleotides leads to improved non-coding RNA gene search.
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Durbin, R., Eddy, S.R., Krogh, A., Mitchison, G.: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge (1998)
Eddy, S.R., Durbin, R.: RNA Sequence Analysis Using Covariance Models. Nucleic Acids Research 22, 2079–2088 (1995)
Karplus, K., Barrett, C., Hughey, R.: Hidden Markov Models for Detecting Remote Protein Homologies. Bioinformatics 14, 846–856 (1998)
Eddy, S.R.: Hidden Markov Models. Curr. Opp. Structural Biology 6, 361–365 (1996)
Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., Bateman, A.: Rfam: Annotating Non-coding RNAs in Complete Genomes. Nucleic Acids Research 33, D121–D124 (2005)
Rfam, R.N.A.: Families Database of Alignments and Covariance Models, version 9.1 (2008), http://rfam.janelia.org
Sjölander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., et al.: Dirichlet Mixtures: a Method for Improving Detection of Weak but Significant Protein Structure Momology. Comp. Appl. Biosci. 12, 327–345 (1996)
Eddy, S.R.: Infernal User’s Guide, version 1.0.2 (2010), http://infernal.rfam.org
Nawrocki, E., Eddy, S.R.: Query-dependent Banding (QDB) for Faster RNA Similarity Searches. PLoS Comp. Bio. 3, 540–554 (2007)
Zucher, M.: Computer Prediction of RNA Structure. Methods Enzymology 180, 262–288 (1989)
Wiese, K.C., Hendricks, A.: A Hybrid Clustering/Evolutionary Algorithm for RNA Folding. In: Symp. Comp. Intelligence Bioinformatics Comp. Biol., pp. 15–21. IEEE Press, New York (2008)
Smith, J.A., Wiese, K.C.: Integrating Thermodynamic and Observed-Frequency Data for Non-coding RNA Gene Search. In: Priami, C., Dressler, F., Akan, O., Ngom, A. (eds.) Trans. Computational Systems Biology X, pp. 124–142. Springer, Berlin (2008)
Vecenie, C., Serra, M.: Stability of RNA Hairpin Loops Closed by AU Base Pairs. Biochemistry 43, 11813–11817 (2004)
Dale, T., Smith, R., Serra, M.: A Test of the Model to Predict Unusually Stable RNA Hairpin Loop Stability. RNA 6, 608–615 (2000)
Serra, M., Little, M., Axenson, T., Schadt, C., Turner, D.: RNA Hairpin Loop Stability Depends on Closing Base Pair. Nucleic Acids Research 21, 3845–3849 (1993)
Serra, M., Axenson, T., Turner, D.: A Model for the Stabilities of RNA Hairpins Based on a Study of the Sequence Dependence of Stability for Hairpins with Six Nucleotides. Biochemistry 33, 14289–14296 (1994)
Giese, R., Beschart, K., Dale, T., Riley, C., Rowan, C., Sprouse, K., Serra, M.: Stability of RNA Hairpins Closed by Wobble Base Pairs. Biochemistry 37, 1094–1100 (1998)
Freier, S., Kierzek, R., Jaeger, J., Sugimoto, N., Caruthers, M., Neilson, T., Turner, D.: Improved Free-Energy Parameters for Predictions of RNA Duplex Stability. Proc. Natl. Acad. Sci. USA 83, 9373–9377 (1986)
Staple, D., Butcher, S.: Pseudoknots: RNA Structures with Diverse Functions. PLoS Bio. 3, 956–959 (2005)
Chomsky, N.: Three Models for the Description of Language. IRE Trans. Information Theory 2, 113–124 (1956)
Gumbel, J.: Statistics of Extremes. Columbia University Press, New York (1958)
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Smith, J. (2010). Joint Loop End Modeling Improves Covariance Model Based Non-coding RNA Gene Search. In: Dijkstra, T.M.H., Tsivtsivadze, E., Marchiori, E., Heskes, T. (eds) Pattern Recognition in Bioinformatics. PRIB 2010. Lecture Notes in Computer Science(), vol 6282. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16001-1_3
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DOI: https://doi.org/10.1007/978-3-642-16001-1_3
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