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Volumn 28, Issue 17, 2012, Pages 2242-2248

Bayesian sampling of evolutionarily conserved rna secondary structures with pseudoknots

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEASE P; RNA; UNTRANSLATED RNA;

EID: 84865546962     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts369     Document Type: Article
Times cited : (6)

References (46)
  • 1
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 2
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • Beaumont, M.A. et al. (2002) Approximate Bayesian computation in population genetics. Genetics, 162, 2025-2035.
    • (2002) Genetics , vol.162 , pp. 2025-2035
    • Beaumont, M.A.1
  • 3
    • 58249121729 scopus 로고    scopus 로고
    • Rnaalifold: improved consensus structure prediction for RNA alignments
    • Bernhart, S.H. et al. (2008) Rnaalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9, 474.
    • (2008) BMC Bioinformatics , vol.9 , pp. 474
    • Bernhart, S.H.1
  • 4
    • 33344469705 scopus 로고    scopus 로고
    • RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers
    • Bindewald, E. and Shapiro, B.A. (2006) RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA, 12, 342-352.
    • (2006) RNA , vol.12 , pp. 342-352
    • Bindewald, E.1    Shapiro, B.A.2
  • 5
    • 78049402859 scopus 로고    scopus 로고
    • Molecular signals of epigenetic states
    • Bonasio, R. et al. (2010) Molecular signals of epigenetic states. Science, 330, 612-616.
    • (2010) Science , vol.330 , pp. 612-616
    • Bonasio, R.1
  • 6
    • 0344298926 scopus 로고    scopus 로고
    • The ribonuclease P database
    • Brown, J.W. (1999) The ribonuclease P database. Nucleic Acids Res., 27, 314.
    • (1999) Nucleic Acids Res , vol.27 , pp. 314
    • Brown, J.W.1
  • 7
    • 51749093577 scopus 로고    scopus 로고
    • Flexstem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space
    • Chen, X. et al. (2008) Flexstem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. Bioinformatics, 24, 1994-2001.
    • (2008) Bioinformatics , vol.24 , pp. 1994-2001
    • Chen, X.1
  • 9
    • 77954816556 scopus 로고    scopus 로고
    • Approximate Bayesian computation (abc) in practice
    • Csilléry, K. et al. (2010) Approximate Bayesian computation (abc) in practice. Trends Ecol. Evol., 25, 410-418.
    • (2010) Trends Ecol. Evol. , vol.25 , pp. 410-418
    • Csilléry, K.1
  • 10
    • 67650727366 scopus 로고    scopus 로고
    • Varna: Interactive drawing and editing of the RNA secondary structure
    • Darty, K. et al. (2009) Varna: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975.
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1
  • 12
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy, S.R. and Durbin, R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088.
    • (1994) Nucleic Acids Res , vol.22 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 13
    • 4444279167 scopus 로고    scopus 로고
    • What is Bayesian statistics? Nat
    • Eddy, S.R. (2004) What is Bayesian statistics? Nat. Biotechnol., 22, 1177-1178.
    • (2004) Biotechnol , vol.22 , pp. 1177-1178
    • Eddy, S.R.1
  • 14
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: a maximum likelihood approach
    • Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17, 368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 15
    • 17144452674 scopus 로고    scopus 로고
    • NMR spectroscopy of RNA
    • Fürtig, B. et al. (2003) NMR spectroscopy of RNA. Chembiochem, 4, 936-962.
    • (2003) Chembiochem , vol.4 , pp. 936-962
    • Fürtig, B.1
  • 16
    • 13344262673 scopus 로고    scopus 로고
    • A comprehensive comparison of comparative RNA structure prediction approaches
    • Gardner, P.P. and Giegerich, R. (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5, 140.
    • (2004) BMC Bioinformatics , vol.5 , pp. 140
    • Gardner, P.P.1    Giegerich, R.2
  • 17
    • 0021518209 scopus 로고
    • Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images
    • Geman, S. and Geman, D. (1984) Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images. IEEE Trans. Pattern Anal. Mach. Intell., 6, 721-741.
    • (1984) IEEE Trans. Pattern Anal. Mach. Intell. , vol.6 , pp. 721-741
    • Geman, S.1    Geman, D.2
  • 18
    • 0035873307 scopus 로고    scopus 로고
    • Discovering common stem-loop motifs in unaligned RNA sequences
    • Gorodkin, J. et al. (2001) Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res., 29, 2135-2144.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2135-2144
    • Gorodkin, J.1
  • 19
    • 0035259427 scopus 로고    scopus 로고
    • New insight into Rnase P RNA structure from comparative analysis of the archaeal RNA
    • Harris, J.K. et al. (2001) New insight into Rnase P RNA structure from comparative analysis of the archaeal RNA. RNA, 7, 220-232.
    • (2001) RNA , vol.7 , pp. 220-232
    • Harris, J.K.1
  • 20
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker, I.L. et al. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol., 319, 1059-1066.
    • (2002) J. Mol. Biol. , vol.319 , pp. 1059-1066
    • Hofacker, I.L.1
  • 21
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • Huelsenbeck, J.P. et al. (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294, 2310-2314.
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1
  • 22
    • 0011450901 scopus 로고
    • An efficient recognition and syntax analysis algorithm for contextfree languages
    • Air Force Cambridge Research Laboratory, Bedford, MA
    • Kasami, T. (1965) An efficient recognition and syntax analysis algorithm for contextfree languages. Technical Report AFCRL-65-758, Air Force Cambridge Research Laboratory, Bedford, MA.
    • (1965) Technical Report AFCRL-65-758
    • Kasami, T.1
  • 23
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S. et al. (1983) Optimization by simulated annealing. Science, 220, 4598, 671-680.
    • (1983) Science , vol.220 , Issue.4598 , pp. 671-680
    • Kirkpatrick, S.1
  • 24
    • 0032796501 scopus 로고    scopus 로고
    • RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
    • Knudsen, B. and Hein, J. (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics, 15, 446-454.
    • (1999) Bioinformatics , vol.15 , pp. 446-454
    • Knudsen, B.1    Hein, J.2
  • 25
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • Knudsen, B. and Hein, J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res., 31, 3423-3428.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 26
    • 0002532056 scopus 로고
    • The estimation of stochastic context-free grammars using the inside-outside algorithm
    • Lari, K. andYoung, S.J. (1990) The estimation of stochastic context-free grammars using the inside-outside algorithm. Comput. Speech Lang., 4, 35-56.
    • (1990) Comput. Speech Lang. , vol.4 , pp. 35-56
    • Lari, K.1    Young, S.J.2
  • 27
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews, B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta., 405, 442-451.
    • (1975) Biochim. Biophys. Acta. , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 28
    • 36448984918 scopus 로고    scopus 로고
    • Predicting RNA secondary structures with pseudoknots by MCMC sampling
    • Metzler, D. and Nebel, M.E. (2008) Predicting RNA secondary structures with pseudoknots by MCMC sampling. J. Math. Biol., 56, 161-181.
    • (2008) J. Math. Biol. , vol.56 , pp. 161-181
    • Metzler, D.1    Nebel, M.E.2
  • 29
    • 34548443728 scopus 로고    scopus 로고
    • Simulfold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework
    • Meyer, I.M. and Miklós, I. (2007) Simulfold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput. Biol., 3, e149.
    • (2007) PLoS Comput. Biol. , vol.3
    • Meyer, I.M.1    Miklós, I.2
  • 31
    • 77953957633 scopus 로고    scopus 로고
    • A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
    • Poliseno, L. et al. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465, 1033-1038.
    • (2010) Nature , vol.465 , pp. 1033-1038
    • Poliseno, L.1
  • 33
    • 5344230543 scopus 로고    scopus 로고
    • (last accessed 6. June 2012)
    • Rambaut, A, Drummond, A. (2007) Tracer v1.4, http://beast.bio.ed.ac.uk/tracer. (last accessed 6. June 2012)
    • (2007) Tracer v1.4
    • Rambaut, A.1    Drummond, A.2
  • 34
    • 13244252326 scopus 로고    scopus 로고
    • Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
    • Reeder, J. and Giegerich, R. (2004) Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics, 5, 104.
    • (2004) BMC Bioinformatics , vol.5 , pp. 104
    • Reeder, J.1    Giegerich, R.2
  • 35
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • Rivas, E. and Eddy, S.R. (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285, 2053-2068.
    • (1999) J. Mol. Biol. , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 36
    • 77950554806 scopus 로고    scopus 로고
    • Kinship in the SRP RNA family
    • Rosenblad, M.A. et al. (2009) Kinship in the SRP RNA family. RNA Biol., 6, 508-516.
    • (2009) RNA Biol , vol.6 , pp. 508-516
    • Rosenblad, M.A.1
  • 37
    • 67650713931 scopus 로고    scopus 로고
    • The structural and functional diversity of metabolitebinding riboswitches
    • Roth, A. and Breaker, R.R. (2009) The structural and functional diversity of metabolitebinding riboswitches. Annu. Rev. Biochem., 78, 305-334.
    • (2009) Annu. Rev. Biochem. , vol.78 , pp. 305-334
    • Roth, A.1    Breaker, R.R.2
  • 38
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    • Ruan, J. et al. (2004) An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics, 20, 58-66.
    • (2004) Bioinformatics , vol.20 , pp. 58-66
    • Ruan, J.1
  • 39
    • 79959465715 scopus 로고    scopus 로고
    • Ipknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
    • Sato, K. et al. (2011) Ipknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics, 27, i85-i93.
    • (2011) Bioinformatics , vol.27
    • Sato, K.1
  • 40
    • 0028512129 scopus 로고
    • A stochastic model for the evolution of autocorrelated DNA sequences
    • Schöniger, M. and von Haeseler, A. (1994) A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylogenet. Evol., 3, 240-247.
    • (1994) Mol. Phylogenet. Evol. , vol.3 , pp. 240-247
    • Schöniger, M.1    von Haeseler, A.2
  • 41
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RaxML web servers
    • Stamatakis, A. et al. (2008) A rapid bootstrap algorithm for the RaxML web servers. Syst. Biol., 57, 758-771.
    • (2008) Syst. Biol. , vol.57 , pp. 758-771
    • Stamatakis, A.1
  • 42
    • 22744455135 scopus 로고    scopus 로고
    • Pseudoknots: RNA structures with diverse functions
    • Staple, D.W. and Butcher, S.E. (2005) Pseudoknots: RNA structures with diverse functions. PLoS Biol., 3, e213.
    • (2005) PLoS Biol , vol.3
    • Staple, D.W.1    Butcher, S.E.2
  • 43
    • 0023672228 scopus 로고
    • Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications
    • Wheeler, W.C. and Honeycutt, R.L. (1988) Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Mol. Biol. Evol., 5, 90-96.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 90-96
    • Wheeler, W.C.1    Honeycutt, R.L.2
  • 44
    • 44349140636 scopus 로고    scopus 로고
    • R-coffee: a method for multiple alignment of non-coding RNA
    • Wilm, A. et al. (2008) R-coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res., 36.
    • (2008) Nucleic Acids Res , vol.36
    • Wilm, A.1
  • 45
    • 49949139581 scopus 로고
    • Recognition and parsing of context-free languages in time n3
    • Younger, D.H. (1967) Recognition and parsing of context-free languages in time n3. Inform. Control, 10, 189-208.
    • (1967) Inform. Control , vol.10 , pp. 189-208
    • Younger, D.H.1
  • 46
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M. and Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
    • (1981) Nucleic Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


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