메뉴 건너뛰기




Volumn 56, Issue 1-2, 2008, Pages 161-181

Predicting RNA secondary structures with pseudoknots by MCMC sampling

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

EID: 36448984918     PISSN: 03036812     EISSN: 14321416     Source Type: Journal    
DOI: 10.1007/s00285-007-0106-6     Document Type: Article
Times cited : (34)

References (62)
  • 1
    • 0041940818 scopus 로고    scopus 로고
    • Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
    • Akutsu T. (2000). Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Appl. Math. 104: 46-62
    • (2000) Discrete Appl. Math. , vol.104 , pp. 46-62
    • Akutsu, T.1
  • 2
    • 0035863762 scopus 로고    scopus 로고
    • The estimation of statistical parameters for local alignment score distributions
    • 2
    • Altschul S.F., Bundschuh R., Olsen R. and Hwa T. (2001). The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Res. 29(2): 351-361
    • (2001) Nucleic Acids Res. , vol.29 , pp. 351-361
    • Altschul, S.F.1    Bundschuh, R.2    Olsen, R.3    Hwa, T.4
  • 3
    • 1842532350 scopus 로고    scopus 로고
    • The Bayesian revolution in genetics
    • 4
    • Beaumont M.A. and Rannala B. (2004). The Bayesian revolution in genetics. Nat. Rev. Genet. 5(4): 251-261
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 251-261
    • Beaumont, M.A.1    Rannala, B.2
  • 4
    • 0344298926 scopus 로고    scopus 로고
    • The Ribonuclease P Database
    • 1
    • Brown J.W. (1999). The Ribonuclease P Database. Nucleic Acids Res. 27(1): 314
    • (1999) Nucleic Acids Res. , vol.27 , pp. 314
    • Brown, J.W.1
  • 5
    • 3543069105 scopus 로고    scopus 로고
    • Stochastic modeling of RNA pseudoknotted structures: A grammatical approach
    • Suppl 1
    • Cai L., Malmberg R.L. and Wu Y. (2003). Stochastic modeling of RNA pseudoknotted structures: a grammatical approach. Bioinformatics 19(Suppl 1): i66-73
    • (2003) Bioinformatics , vol.19 , pp. 66-73
    • Cai, L.1    Malmberg, R.L.2    Wu, Y.3
  • 6
    • 33344474707 scopus 로고    scopus 로고
    • Statistical and Bayesian approaches to RNA secondary structure prediction
    • 3
    • Ding Y. (2006). Statistical and Bayesian approaches to RNA secondary structure prediction. RNA 12(3): 323-331
    • (2006) RNA , vol.12 , pp. 323-331
    • Ding, Y.1
  • 7
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Web Server issue
    • Ding Y., Chan C.Y. and Lawrence C.E. (2004). Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32(Web Server issue): W135-141
    • (2004) Nucleic Acids Res. , vol.32 , pp. 135-141
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 8
    • 23644448438 scopus 로고    scopus 로고
    • RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
    • 8
    • Ding Y., Chan C.Y. and Lawrence C.E. (2005). RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11(8): 1157-1166
    • (2005) RNA , vol.11 , pp. 1157-1166
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 9
    • 33646784027 scopus 로고    scopus 로고
    • Clustering of RNA secondary structures with application to messenger RNAs
    • 3
    • Ding Y., Chan C.Y. and Lawrence C.E. (2006). Clustering of RNA secondary structures with application to messenger RNAs. J. Mol. Biol. 359(3): 554-571
    • (2006) J. Mol. Biol. , vol.359 , pp. 554-571
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 10
    • 0033563515 scopus 로고    scopus 로고
    • A Bayesian statistical algorithm for RNA secondary structure prediction
    • 3-4
    • Ding Y. and Lawrence C.E. (1999). A Bayesian statistical algorithm for RNA secondary structure prediction. Comput. Chem. 23(3-4): 387-400
    • (1999) Comput. Chem. , vol.23 , pp. 387-400
    • Ding, Y.1    Lawrence, C.E.2
  • 11
    • 0346888665 scopus 로고    scopus 로고
    • A statistical sampling algorithm for RNA secondary structure prediction
    • 24
    • Ding Y. and Lawrence C.E. (2003). A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res. 31(24): 7280-7301
    • (2003) Nucleic Acids Res. , vol.31 , pp. 7280-7301
    • Ding, Y.1    Lawrence, C.E.2
  • 13
    • 0043285072 scopus 로고    scopus 로고
    • A partition function algorithm for nucleic acid secondary structure including pseudoknots
    • 13
    • Dirks R.M. and Pierce N.A. (2003). A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem. 24(13): 1664-1677
    • (2003) J. Comput. Chem. , vol.24 , pp. 1664-1677
    • Dirks, R.M.1    Pierce, N.A.2
  • 14
    • 3042554001 scopus 로고    scopus 로고
    • An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots
    • 10
    • Dirks R.M. and Pierce N.A. (2004). An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J. Comput. Chem. 25(10): 1295-1304
    • (2004) J. Comput. Chem. , vol.25 , pp. 1295-1304
    • Dirks, R.M.1    Pierce, N.A.2
  • 15
    • 13344279384 scopus 로고    scopus 로고
    • Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
    • Doshi K.J., Cannone J.J., Cobaugh C.W. and Gutell R.R. (2004). Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics 5: 105
    • (2004) BMC Bioinformatics , vol.5 , pp. 105
    • Doshi, K.J.1    Cannone, J.J.2    Cobaugh, C.W.3    Gutell, R.R.4
  • 16
    • 13244260785 scopus 로고    scopus 로고
    • Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
    • Dowell R.D. and Eddy S.R. (2004). Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics 5: 71
    • (2004) BMC Bioinformatics , vol.5 , pp. 71
    • Dowell, R.D.1    Eddy, S.R.2
  • 18
    • 4444279167 scopus 로고    scopus 로고
    • What is Bayesian statistics?
    • 9
    • Eddy S.R. (2004). What is Bayesian statistics?. Nat. Biotechnol. 22(9): 1177-1178
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1177-1178
    • Eddy, S.R.1
  • 19
    • 25144452234 scopus 로고    scopus 로고
    • Simultaneous statistical multiple alignment and phylogeny reconstruction
    • 4
    • Fleissner R., Metzler D. and von Haeseler A. (2005). Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst. Biol. 54(4): 548-561
    • (2005) Syst. Biol. , vol.54 , pp. 548-561
    • Fleissner, R.1    Metzler, D.2    Von Haeseler, A.3
  • 21
    • 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
  • 22
    • 0021518209 scopus 로고
    • Stochastic relaxation, Gibbs distribution and the Bayesian restoration of images
    • Geman S. and Geman D. (1984). Stochastic relaxation, Gibbs distribution 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
  • 23
    • 36448985451 scopus 로고    scopus 로고
    • GPL.: The GNU Public License. Available in full from http://www.fsf.org/ copyleft/gpl.html (2000)
    • (2000) GPL.: The GNU Public License
  • 25
    • 77956890234 scopus 로고
    • Monte Carlo Sampling Methods Using Markov Chains and Their Applications
    • Hastings W.K. (1970). Monte Carlo Sampling Methods Using Markov Chains and Their Applications. Biometrika 57: 97-109
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 26
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • 13
    • Hofacker I.L. (2003). Vienna RNA secondary structure server. Nucleic Acids Res 31(13): 3429-3431
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 28
    • 52449148668 scopus 로고
    • The role of compensatory neutral mutations in molecular evolution
    • Kimura M. (1985). The role of compensatory neutral mutations in molecular evolution. J. Genet. 64: 7-19
    • (1985) J. Genet. , vol.64 , pp. 7-19
    • Kimura, M.1
  • 29
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick S., Gelatt C.D. and Vecchi M.P. (1983). Optimization by simulated annealing. Science 220: 671-680
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 30
    • 0032796501 scopus 로고    scopus 로고
    • RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
    • 6
    • Knudsen B. and Hein J. (1999). RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 15(6): 446-454
    • (1999) Bioinformatics , vol.15 , pp. 446-454
    • Knudsen, B.1    Hein, J.2
  • 31
    • 13744249396 scopus 로고    scopus 로고
    • A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation
    • 2
    • Layton D.M. and Bundschuh R. (2005). A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation. Nucleic Acids Res. 33(2): 519-524
    • (2005) Nucleic Acids Res. , vol.33 , pp. 519-524
    • Layton, D.M.1    Bundschuh, R.2
  • 34
    • 0033709625 scopus 로고    scopus 로고
    • RNA pseudoknot prediction in energy-based models
    • 3-4
    • Lyngso R.B. and Pedersen C.N. (2000). RNA pseudoknot prediction in energy-based models. J. Comput. Biol. 7(3-4): 409-427
    • (2000) J. Comput. Biol. , vol.7 , pp. 409-427
    • Lyngso, R.B.1    Pedersen, C.N.2
  • 35
    • 3342977915 scopus 로고    scopus 로고
    • Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
    • 8
    • Mathews D.H. (2004). Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA 10(8): 1178-1190
    • (2004) RNA , vol.10 , pp. 1178-1190
    • Mathews, D.H.1
  • 36
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • 6-7
    • McCaskill J.S. (1990). The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29(6-7): 1105-1119
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 38
    • 0037339432 scopus 로고    scopus 로고
    • Statistical alignment based on fragment insertion and deletion models
    • 4
    • Metzler D. (2003). Statistical alignment based on fragment insertion and deletion models. Bioinformatics 19(4): 490-499
    • (2003) Bioinformatics , vol.19 , pp. 490-499
    • Metzler, D.1
  • 39
    • 33745321162 scopus 로고    scopus 로고
    • Robust E-values for gapped local alignments
    • 4
    • Metzler D. (2006). Robust E-values for gapped local alignments. J. Comput. Biol. 13(4): 882-96
    • (2006) J. Comput. Biol. , vol.13 , pp. 882-96
    • Metzler, D.1
  • 40
    • 17944382496 scopus 로고    scopus 로고
    • Assessing variability by joint sampling of alignments and mutation rates
    • 6
    • Metzler D., Fleissner R., Wakolbinger A. and von Haeseler A. (2001). Assessing variability by joint sampling of alignments and mutation rates. J. Mol. Evol. 53(6): 660-669
    • (2001) J. Mol. Evol. , vol.53 , pp. 660-669
    • Metzler, D.1    Fleissner, R.2    Wakolbinger, A.3    Von Haeseler, A.4
  • 41
    • 25144470400 scopus 로고    scopus 로고
    • Stochastic insertion-deletion processes and statistical sequence alignment
    • Deuschel, J.D., Greven, A. (eds.) Springer, Heidelberg
    • Metzler, D., Fleißner, R., Wakolbinger, A., von Haeseler, A.: Stochastic insertion-deletion processes and statistical sequence alignment. In: Deuschel, J.D., Greven, A. (eds.) Interacting Stochastic Systems. Springer, Heidelberg (2005)
    • (2005) Interacting Stochastic Systems
    • Metzler, D.1    Fleißner, R.2    Wakolbinger, A.3    Von Haeseler, A.4
  • 44
    • 2442648081 scopus 로고    scopus 로고
    • Identifying good predictions of RNA secondary structure
    • Nebel, M.E.: Identifying good predictions of RNA secondary structure. Pac Symp Biocomput, pp. 423-434 (2004)
    • (2004) Pac Symp Biocomput , pp. 423-434
    • Nebel, M.E.1
  • 46
    • 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
  • 47
    • 25844447772 scopus 로고    scopus 로고
    • HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots
    • 10
    • Ren J., Rastegari B., Condon A. and Hoos H.H. (2005). HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA 11(10): 1494-1504
    • (2005) RNA , vol.11 , pp. 1494-1504
    • Ren, J.1    Rastegari, B.2    Condon, A.3    Hoos, H.H.4
  • 48
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • 5
    • Rivas E. and Eddy S.R. (1999). A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285(5): 2053-2068
    • (1999) J. Mol. Biol. , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 49
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the prediction of RNA secondary structures with~pseudoknots
    • 1
    • Ruan J., Stormo G.D. and Zhang W. (2004). An iterated loop matching approach to the prediction of RNA secondary structures with~pseudoknots. Bioinformatics 20(1): 58-66
    • (2004) Bioinformatics , vol.20 , pp. 58-66
    • Ruan, J.1    Stormo, G.D.2    Zhang, W.3
  • 50
    • 0029975949 scopus 로고    scopus 로고
    • Description of RNA folding by "simulated annealing"
    • 1
    • Schmitz M. and Steger G. (1996). Description of RNA folding by "simulated annealing". J. Mol. Biol. 255(1): 254-266
    • (1996) J. Mol. Biol. , vol.255 , pp. 254-266
    • Schmitz, M.1    Steger, G.2
  • 51
    • 0017194487 scopus 로고
    • Mechanisms of chain folding in nucleic acids. the (omega, omega) plot and its correlation to the nucleotide geometry in yeast tRNAPhe
    • 10
    • Sundaralingam M., Mizuno H., Stout C.D., Rao S.T., Liedman M. and Yathindra N. (1976). Mechanisms of chain folding in nucleic acids. The (omega, omega) plot and its correlation to the nucleotide geometry in yeast tRNAPhe. Nucleic Acids Res. 3(10): 2471-2484
    • (1976) Nucleic Acids Res. , vol.3 , pp. 2471-2484
    • Sundaralingam, M.1    Mizuno, H.2    Stout, C.D.3    Rao, S.T.4    Liedman, M.5    Yathindra, N.6
  • 55
    • 34248222805 scopus 로고    scopus 로고
    • Computing the parition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model
    • in press
    • Waldispühl, J., Clote, P.: Computing the parition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model. J. Comput. Biol. (2007, in press)
    • (2007) J. Comput. Biol.
    • Waldispühl, J.1    Clote, P.2
  • 56
    • 0028000994 scopus 로고
    • Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
    • 20
    • Walter A.E., Turner D.H., Kim J., Lyttle M.H., Muller P., Mathews D.H. and Zuker M. (1994). Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl. Acad. Sci. USA 91(20): 9218-9222
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 9218-9222
    • Walter, A.E.1    Turner, D.H.2    Kim, J.3    Lyttle, M.H.4    Muller, P.5    Mathews, D.H.6    Zuker, M.7
  • 57
    • 0001509501 scopus 로고
    • Secondary Structure of Single-Stranded Nucleic Acids
    • Waterman M.S. (1978). Secondary Structure of Single-Stranded Nucleic Acids. Adv. Math. Suppl. Stud. 1: 167-212
    • (1978) Adv. Math. Suppl. Stud. , vol.1 , pp. 167-212
    • Waterman, M.S.1
  • 61
    • 0347364655 scopus 로고    scopus 로고
    • Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
    • 26
    • Xayaphoummine A., Bucher T., Thalmann F. and Isambert H. (2003). Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc. Natl. Acad. Sci. USA 100(26): 15310-15315
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15310-15315
    • Xayaphoummine, A.1    Bucher, T.2    Thalmann, F.3    Isambert, H.4
  • 62
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • 1
    • Zuker M. and Stiegler P. (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9(1): 133-148
    • (1981) Nucleic Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.