메뉴 건너뛰기




Volumn 285, Issue 5, 1999, Pages 2053-2068

A dynamic programming algorithm for RNA structure prediction including pseudoknots

Author keywords

Dynamic programming; Pseudoknots; RNA; Secondary structure prediction; Thermodynamic stability

Indexed keywords

RNA;

EID: 0033524952     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2436     Document Type: Article
Times cited : (616)

References (44)
  • 1
    • 0025315854 scopus 로고
    • Prediction of RNA secondary structure, including pseudoknotting, by computer simulation
    • Abrahams J. P., van der Berg M., van Batenburg E., Pleij C. W. A. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucl. Acids Res. 18:1990;3035-3044.
    • (1990) Nucl. Acids Res. , vol.18 , pp. 3035-3044
    • Abrahams, J.P.1    Van Der Berg, M.2    Van Batenburg, E.3    Pleij, C.W.A.4
  • 4
    • 0030310297 scopus 로고    scopus 로고
    • RNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search
    • Brown M. RNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search. Pacific Symposium on Biocomputing 1996. 1996.
    • (1996) Pacific Symposium on Biocomputing 1996
    • Brown, M.1
  • 5
    • 0029185452 scopus 로고
    • Graph-theoretic approach to RNA modeling using comparative data
    • Rawling C. et al. AAAI Press
    • Cary R. B., Stormo G. D. Graph-theoretic approach to RNA modeling using comparative data. Rawling C. et al. ISMB-95. 1995;75-80 AAAI Press.
    • (1995) ISMB-95 , pp. 75-80
    • Cary, R.B.1    Stormo, G.D.2
  • 6
    • 0023316092 scopus 로고
    • 3-D graphics modeling of the tRNA-like 3′ end of turnip yellow mosaic virus RNA: Structural and functional implications
    • Dumas P., Moras D., Florentz C., Giegé R., Verlaan P., van Belkum A., Pleij C. W. A. 3-D graphics modeling of the tRNA-like 3′ end of turnip yellow mosaic virus RNA: structural and functional implications. J. Biomol. Struct. Dynam. 4:1987;707-728.
    • (1987) J. Biomol. Struct. Dynam. , vol.4 , pp. 707-728
    • Dumas, P.1    Moras, D.2    Florentz, C.3    Giegé, R.4    Verlaan, P.5    Van Belkum, A.6    Pleij, C.W.A.7
  • 8
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy S. R., Durbin R. RNA sequence analysis using covariance models. Nucl. Acids Res. 22:1994;2079-2088.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 9
    • 0001214263 scopus 로고
    • Maximum matching and polyhedron with 0, 1-vertices
    • Edmonds J. Maximum matching and polyhedron with 0, 1-vertices. J. Res. Nat. Bur. Stand. 69B:1965;125-130.
    • (1965) J. Res. Nat. Bur. Stand. , vol.69 , pp. 125-130
    • Edmonds, J.1
  • 10
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferré-D'Amaré A. R., Zhou K., Doudna J. A. Crystal structure of a hepatitis delta virus ribozyme. Nature. 395:1998;567-574.
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferré-D'Amaré, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 12
    • 0016943409 scopus 로고
    • An efficient implementation of Edmonds' algorithm for maximum matching on graphs
    • Gabow H. N. An efficient implementation of Edmonds' algorithm for maximum matching on graphs. J. Asc. Com. Mach. 23:1976;221-234.
    • (1976) J. Asc. Com. Mach. , vol.23 , pp. 221-234
    • Gabow, H.N.1
  • 13
    • 0027932176 scopus 로고
    • Thermodynamics of folding a pseudoknotted mRNA fragment
    • Gluick T. C., Draper D. E. Thermodynamics of folding a pseudoknotted mRNA fragment. J. Mol. Biol. 241:1994;246-262.
    • (1994) J. Mol. Biol. , vol.241 , pp. 246-262
    • Gluick, T.C.1    Draper, D.E.2
  • 14
    • 0018462972 scopus 로고
    • Sequence of 1000 nucleotides at the 3′ end of tobacco mosaic virus RNA
    • Guilley H., Jonard G., Kukla B., Richards K. E. Sequence of 1000 nucleotides at the 3′ end of tobacco mosaic virus RNA. Nucl. Acids Res. 6:1979;1287-1308.
    • (1979) Nucl. Acids Res. , vol.6 , pp. 1287-1308
    • Guilley, H.1    Jonard, G.2    Kukla, B.3    Richards, K.E.4
  • 15
    • 0029061125 scopus 로고
    • The computer simulation of RNA folding pathways using a genetic algorithm
    • Gultyaev A. P., van Batenburg F. H., Pleij C. W. A. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:1995;37-51.
    • (1995) J. Mol. Biol. , vol.250 , pp. 37-51
    • Gultyaev, A.P.1    Van Batenburg, F.H.2    Pleij, C.W.A.3
  • 16
    • 0031576996 scopus 로고    scopus 로고
    • Assessing the reliability of RNA folding using statistical mechanics
    • Huynen M., Gutell R., Konings D. Assessing the reliability of RNA folding using statistical mechanics. J. Mol. Biol. 267:1997;1104-1112.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1104-1112
    • Huynen, M.1    Gutell, R.2    Konings, D.3
  • 17
  • 18
    • 0030333721 scopus 로고    scopus 로고
    • A grammar-based unification of several alignments and folding algorithms
    • Rawlings C. et al. AAAI Press
    • Lefebvre F. A grammar-based unification of several alignments and folding algorithms. Rawlings C. et al. ISMB-96. 1996;143-154 AAAI Press.
    • (1996) ISMB-96 , pp. 143-154
    • Lefebvre, F.1
  • 19
    • 0000923493 scopus 로고    scopus 로고
    • An updated recursive algorithm for RNA secondary structure prediction with improved free energy parameters
    • N. B. Leontis, & J. Jr. SantaLucia. American Chemical Society
    • Mathews D. H., Andre T. C., Kim J., Turner D. H., Zuker M. An updated recursive algorithm for RNA secondary structure prediction with improved free energy parameters. Leontis N. B., SantaLucia J. Jr. Molecular Modeling of Nucleic Acids. 1998;American Chemical Society.
    • (1998) Molecular Modeling of Nucleic Acids
    • Mathews, D.H.1    Andre, T.C.2    Kim, J.3    Turner, D.H.4    Zuker, M.5
  • 20
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair bindings probabilities for RNA secondary structure
    • McCaskill J. S. The equilibrium partition function and base pair bindings probabilities for RNA secondary structure. Biopolymers. 29:1990;1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 21
    • 0030813152 scopus 로고    scopus 로고
    • RAGA: RNA sequence alignment by genetic algorithm
    • Notredame C., O'Brien E. A., Higgins D. G. RAGA: RNA sequence alignment by genetic algorithm. Nucl. Acids Res. 25:1997;4570-4580.
    • (1997) Nucl. Acids Res. , vol.25 , pp. 4570-4580
    • Notredame, C.1    O'Brien, E.A.2    Higgins, D.G.3
  • 23
    • 0022423219 scopus 로고
    • A new principle of RNA folding based on pseudoknotting
    • Pleij C. W., Rietveld K., Bosch L. A new principle of RNA folding based on pseudoknotting. Nucl. Acids Res. 13:1985;1717-1731.
    • (1985) Nucl. Acids Res. , vol.13 , pp. 1717-1731
    • Pleij, C.W.1    Rietveld, K.2    Bosch, L.3
  • 25
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protosequence problems
    • Sankoff D. Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math. 45:1985;810-825.
    • (1985) SIAM J. Appl. Math. , vol.45 , pp. 810-825
    • Sankoff, D.1
  • 26
    • 0028196714 scopus 로고
    • From sequences to shapes and back: A case study in RNA secondary structure
    • Schuster P., Fontana W., Stadler P. F., Hofacker I. L. From sequences to shapes and back: a case study in RNA secondary structure. Proc. Roy. Soc. ser. B. 255:1994;279-284.
    • (1994) Proc. Roy. Soc. Ser. B , vol.255 , pp. 279-284
    • Schuster, P.1    Fontana, W.2    Stadler, P.F.3    Hofacker, I.L.4
  • 27
    • 0030968993 scopus 로고    scopus 로고
    • RNA structures and folding: From conventional to new issues in structure predictions
    • Schuster P., Fontana W., Stadler P. F., Renner A. RNA structures and folding: from conventional to new issues in structure predictions. Curr. Opin. Struct. Biol. 7:1997;229-235.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 229-235
    • Schuster, P.1    Fontana, W.2    Stadler, P.F.3    Renner, A.4
  • 28
    • 0029100233 scopus 로고
    • Predicting the thermodynamic properties of RNA
    • Serra M. J., Turner D. H. Predicting the thermodynamic properties of RNA. Methods Enzymol. 259:1995;242-261.
    • (1995) Methods Enzymol. , vol.259 , pp. 242-261
    • Serra, M.J.1    Turner, D.H.2
  • 29
    • 0027244036 scopus 로고
    • Compilation of RNA sequences and sequences of tRNA genes
    • Steinberg S., Misch A., Sprinzl M. Compilation of RNA sequences and sequences of tRNA genes. Nucl. Acids Res. 21:1993;3011-3015.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 3011-3015
    • Steinberg, S.1    Misch, A.2    Sprinzl, M.3
  • 30
    • 0030632075 scopus 로고    scopus 로고
    • Automated alignment of RNA sequences to pseudoknotted structures
    • Tabaska J. E., Stormo G. D. Automated alignment of RNA sequences to pseudoknotted structures. ISMB-97. 5:1997;311-318.
    • (1997) ISMB-97 , vol.5 , pp. 311-318
    • Tabaska, J.E.1    Stormo, G.D.2
  • 31
    • 0031730497 scopus 로고    scopus 로고
    • An RNA folding method capable of identifying pseudoknots and base triples
    • Tabaska J. E., Cary R. B., Gabow H. N., Stormo G. D. An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics. 8:1998;691-699.
    • (1998) Bioinformatics , vol.8 , pp. 691-699
    • Tabaska, J.E.1    Cary, R.B.2    Gabow, H.N.3    Stormo, G.D.4
  • 32
    • 0026483177 scopus 로고
    • Structural and functional aspects of RNA pseudoknots
    • ten Dam E., Pleij K., Draper D. Structural and functional aspects of RNA pseudoknots. Biochemistry. 31:1992;11665-11676.
    • (1992) Biochemistry , vol.31 , pp. 11665-11676
    • Ten Dam, E.1    Pleij, K.2    Draper, D.3
  • 33
    • 0026651981 scopus 로고
    • RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase
    • Tuerk C., MacDougal S., Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl Acad. Sci. USA. 89:1992;6988-6992.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 6988-6992
    • Tuerk, C.1    MacDougal, S.2    Gold, L.3
  • 34
    • 0029025720 scopus 로고
    • An APL-programmed genetic algorithm for the prediction of RNA secondary structure
    • van Batenburg F. H. D., Gultyaev A. P., Pleij C. W. A. An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J. Theor. Biol. 174:1995;269-280.
    • (1995) J. Theor. Biol. , vol.174 , pp. 269-280
    • Van Batenburg, F.H.D.1    Gultyaev, A.P.2    Pleij, C.W.A.3
  • 35
    • 0022423674 scopus 로고
    • Five pseudoknots are present at the 204 nucleotides long 3′ non coding region of tobacco mosaic virus RNA
    • Van Belkum A., Abrahams J. P., Pleij C. W. A., Bosch L. Five pseudoknots are present at the 204 nucleotides long 3′ non coding region of tobacco mosaic virus RNA. Nucl. Acids Res. 13:1985;7673-7686.
    • (1985) Nucl. Acids Res. , vol.13 , pp. 7673-7686
    • Van Belkum, A.1    Abrahams, J.P.2    Pleij, C.W.A.3    Bosch, L.4
  • 36
    • 0001254342 scopus 로고
    • Structural similarities among valine-accepting tRNA-like structures in tymoviral RNAs and elongator tRNAs
    • Van Belkum A., Bingkun J., Pleij C. W. A., Bosch L. Structural similarities among valine-accepting tRNA-like structures in tymoviral RNAs and elongator tRNAs. Biochemistry. 26:1987;1144-1151.
    • (1987) Biochemistry , vol.26 , pp. 1144-1151
    • Van Belkum, A.1    Bingkun, J.2    Pleij, C.W.A.3    Bosch, L.4
  • 37
    • 0028000994 scopus 로고
    • Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
    • Walter A., Turner D., Kim J., Lyttle M., Müller P., Mathews D., Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl Acad. Sci. USA. 91:1994;9218-9222.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 9218-9222
    • Walter, A.1    Turner, D.2    Kim, J.3    Lyttle, M.4    Müller, P.5    Mathews, D.6    Zuker, M.7
  • 38
    • 0002277269 scopus 로고
    • Probing RNA structure, function, and history by comparative analysis
    • R. F. Gesteland, & J. F. Atkins. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
    • Woese C. R., Pace N. R. Probing RNA structure, function, and history by comparative analysis. Gesteland R. F., Atkins J. F. The RNA World. 1993;91-117 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
    • (1993) The RNA World , pp. 91-117
    • Woese, C.R.1    Pace, N.R.2
  • 39
    • 0025113514 scopus 로고
    • RNA pseudoknots: Stability and loop size requirements
    • Wyatt J. R., Puglisi J. D., Tinoco I. Jr. RNA pseudoknots: stability and loop size requirements. J. Mol Biol. 214:1990;455-470.
    • (1990) J. Mol Biol. , vol.214 , pp. 455-470
    • Wyatt, J.R.1    Puglisi, J.D.2    Tinoco I., Jr.3
  • 40
    • 0024806949 scopus 로고
    • Computer prediction of RNA structure
    • Zuker M. Computer prediction of RNA structure. Methods Enzymol. 180:1989a;262-288.
    • (1989) Methods Enzymol. , vol.180 , pp. 262-288
    • Zuker, M.1
  • 41
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989b;48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 42
    • 0029131459 scopus 로고
    • "well-determined" regions in RNA secondary structure prediction: Analysis of small subunit ribosomal RNA
    • Zuker M. "Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA. Nucl. Acids Res. 23:1995;2791-2798.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 2791-2798
    • Zuker, M.1
  • 43
    • 0000616205 scopus 로고
    • RNA secondary structure and their prediction
    • Zuker M., Sankoff D. RNA secondary structure and their prediction. Bull. Math. Biol. 46:1984;591-621.
    • (1984) Bull. Math. Biol. , vol.46 , pp. 591-621
    • Zuker, M.1    Sankoff, D.2
  • 44
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9:1981;133-148.
    • (1981) Nucl. Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.