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Volumn 20, Issue 1, 2004, Pages 58-66

An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BASE PAIRING; CONTROLLED STUDY; GENETIC ALGORITHM; INTERMETHOD COMPARISON; PREDICTION; PRIORITY JOURNAL; PROTEIN FAMILY; RNA SEQUENCE; RNA STRUCTURE; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; THERMODYNAMICS;

EID: 0347724163     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg373     Document Type: Article
Times cited : (197)

References (41)
  • 1
    • 0025315854 scopus 로고
    • Prediction of RNA secondary structure, including pseudoknotting, by computer simulation
    • Abrahams,J., van den Berg,M., van Batenburg,E. and Pleij,C. (1990) Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res., 18, 3035-3344.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 3035-3344
    • Abrahams, J.1    van den Berg, M.2    van Batenburg, E.3    Pleij, C.4
  • 3
    • 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, 45-62.
    • (2000) Discrete Appl.Math. , vol.104 , pp. 45-62
    • Akutsu, T.1
  • 4
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: An overview
    • Baldi,P., Brunak,S., Chauvin,Y., Andersen,C. and Nielsen,H. (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics, 16, 412-424.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.4    Nielsen, H.5
  • 5
    • 0035253413 scopus 로고    scopus 로고
    • Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching
    • Barrette,I., Poisson,G., Gendron,P. and Major,F. (2001) Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching. Nucleic Acids Res., 29, 753-778.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 753-778
    • Barrette, I.1    Poisson, G.2    Gendron, P.3    Major, F.4
  • 6
    • 2942571539 scopus 로고    scopus 로고
    • The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other rnas
    • Cannone,J., Subramanian,S., Schnare,M., Collett,J., D'Souza,L., Du,Y., Feng,B., Lin,N., Madabusi,L., Muller,K. et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other rnas. BMC Bioinformatics, 3, 2.
    • (2002) BMC Bioinformatics , vol.3 , pp. 2
    • Cannone, J.1    Subramanian, S.2    Schnare, M.3    Collett, J.4    D'Souza, L.5    Du, Y.6    Feng, B.7    Lin, N.8    Madabusi, L.9    Muller, K.10
  • 7
    • 0029185452 scopus 로고
    • Graph-theoretic approach to RNA modeling using comparative data
    • Cary,R. and Stormo,G. (1995) Graph-theoretic approach to RNA modeling using comparative data. Proc. Int. Conf. Intell. Syst. Mol. Biol., 3, 75-80.
    • (1995) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.3 , pp. 75-80
    • Cary, R.1    Stormo, G.2
  • 8
    • 0034598919 scopus 로고    scopus 로고
    • Secondary structure of vertebrate telomerase RNA
    • Chen,J., Blasco,M. and Greider,C. (2000) Secondary structure of vertebrate telomerase RNA. Cell, 100, 503-514.
    • (2000) Cell , vol.100 , pp. 503-514
    • Chen, J.1    Blasco, M.2    Greider, C.3
  • 9
    • 0025832114 scopus 로고
    • Inferring consensus structure from nucleic acid sequences
    • Chiu,D. and Kolodziejczak,T. (1991) Inferring consensus structure from nucleic acid sequences. Comput. Appl. Biosci., 7, 347-352.
    • (1991) Comput. Appl. Biosci. , vol.7 , pp. 347-352
    • Chiu, D.1    Kolodziejczak, T.2
  • 10
    • 0026483177 scopus 로고
    • Structural and functional aspects of RNA pseudoknots
    • Dam,E., Pleij,K. and Draper,D. (1992) Structural and functional aspects of RNA pseudoknots. Biochemistry, 31, 11665-11676.
    • (1992) Biochemistry , vol.31 , pp. 11665-11676
    • Dam, E.1    Pleij, K.2    Draper, D.3
  • 11
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy,S. 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.1    Durbin, R.2
  • 12
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferre-D'Amare,A., Zhou,K. and Doudna,J. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature, 395, 567-574.
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferre-D'Amare, A.1    Zhou, K.2    Doudna, J.3
  • 14
    • 0003603813 scopus 로고
    • Computers and Intractability: A Guide to the Theory of NP-Completeness
    • Freeman, San Francisco
    • Garey,M. and Johnson,D. (1979) Computers and Intractability: A Guide to the Theory of NP-Completeness. Freeman, San Francisco.
    • (1979)
    • Garey, M.1    Johnson, D.2
  • 15
    • 0030812919 scopus 로고    scopus 로고
    • Finding the most significant common sequence and structure motifs in a set of RNA sequences
    • Gorodkin,J., Heyer,L. and Stormo,G. (1997) Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res., 25, 3724-3732.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3724-3732
    • Gorodkin, J.1    Heyer, L.2    Stormo, G.3
  • 17
    • 0030310471 scopus 로고    scopus 로고
    • Using multiple alignments and phylogenetic trees to detect RNA secondary structure
    • Gulko,B. and Haussler,D. (1996) Using multiple alignments and phylogenetic trees to detect RNA secondary structure. Proc. Pac. Symp. Biocomput., 1, 350-367.
    • (1996) Proc. Pac. Symp. Biocomput. , vol.1 , pp. 350-367
    • Gulko, B.1    Haussler, D.2
  • 18
    • 0029061125 scopus 로고
    • The computer simulation of RNA folding pathways using a genetic algorithm
    • Gultyaev,A., van Batenburg,F.H. and Pleij,C. (1995) The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol., 250, 37-51.
    • (1995) J. Mol. Biol. , vol.250 , pp. 37-51
    • Gultyaev, A.1    van Batenburg, F.H.2    Pleij, C.3
  • 19
    • 0026466830 scopus 로고
    • Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods
    • Gutell,R., Power,A., Hertz,G., Putz,E. and Stormo,G. (1992) Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res., 20, 5785-5795.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 5785-5795
    • Gutell, R.1    Power, A.2    Hertz, G.3    Putz, E.4    Stormo, G.5
  • 20
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker,I., Fekete,M. and Stadler,P. (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.1    Fekete, M.2    Stadler, P.3
  • 22
    • 0033054042 scopus 로고    scopus 로고
    • RNA secondary structure prediction based on free energy and phylogenetic analysis
    • Juan,V. and Wilson,C. (1999) RNA secondary structure prediction based on free energy and phylogenetic analysis. J. Mol. Biol., 289, 935-947.
    • (1999) J. Mol. Biol. , vol.289 , pp. 935-947
    • Juan, V.1    Wilson, C.2
  • 24
    • 0033230822 scopus 로고    scopus 로고
    • ConStruct: A tool for thermodynamic controlled prediction of conserved secondary structure
    • Luck,R., Graf,S. and Steger,G. (1999) ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure. Nucleic Acids Res., 27, 4208-4217.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4208-4217
    • Luck, R.1    Graf, S.2    Steger, G.3
  • 25
    • 0033705815 scopus 로고    scopus 로고
    • Pseudoknots in RNA secondary structures
    • Proceedings of the fourth annual international Conference on Computational Molecular Biology, ACM Press
    • Lyngso,R. and Pedersen,C. (2000a) Pseudoknots in RNA secondary structures. Proceedings of the fourth annual international Conference on Computational Molecular Biology, pp. 201-209. ACM Press.
    • (2000) , pp. 201-209
    • Lyngso, R.1    Pedersen, C.2
  • 26
    • 0033709625 scopus 로고    scopus 로고
    • RNA pseudoknot prediction in energy-based models
    • Lyngso,R. and Pedersen,C. (2000b) RNA pseudoknot prediction in energy-based models. J. Comput. Biol., 7, 409-427.
    • (2000) J. Comput. Biol. , vol.7 , pp. 409-427
    • Lyngso, R.1    Pedersen, C.2
  • 27
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews,D., Sabina,J., Zuker,M. and Turner,D. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.1    Sabina, J.2    Zuker, M.3    Turner, D.4
  • 28
    • 0036295198 scopus 로고    scopus 로고
    • Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
    • Mathews,D. and Turner,D. (2002) Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol., 317, 191-203.
    • (2002) J. Mol. Biol. , vol.317 , pp. 191-203
    • Mathews, D.1    Turner, D.2
  • 30
    • 0020490476 scopus 로고
    • The tRNA-like structure at the 3′ terminus of turnip yellow mosaic virus RNA: Differences and similarities with canonical tRNA
    • Rietveld,K., Poelgeest,R.V., Pleij,C., Boom,J.V. and Bosch,L. (1982) The tRNA-like structure at the 3′ terminus of turnip yellow mosaic virus RNA: differences and similarities with canonical tRNA. Nucleic Acids Res., 10, 1929-1946.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 1929-1946
    • Rietveld, K.1    Poelgeest, R.V.2    Pleij, C.3    Boom, J.V.4    Bosch, L.5
  • 31
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • Rivas,E. and Eddy,S. (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.2
  • 33
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protosequence problems
    • Sankoff,D. (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math., 45, 810-825.
    • (1985) SIAM J. Appl. Math. , vol.45 , pp. 810-825
    • Sankoff, D.1
  • 34
    • 0031730497 scopus 로고    scopus 로고
    • An RNA folding method capable of identifying pseudoknots and base triples
    • Tabaska,J., Cary,R., Gabow,H. and Stormo,G. (1998) An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics, 14, 691-699.
    • (1998) Bioinformatics , vol.14 , pp. 691-699
    • Tabaska, J.1    Cary, R.2    Gabow, H.3    Stormo, G.4
  • 35
    • 0026651981 scopus 로고
    • RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase
    • Tuerk,C., MacDougal,S. and Gold,L. (1992) RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl Acad. Sci. USA, 89, 6988-6992.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 6988-6992
    • Tuerk, C.1    MacDougal, S.2    Gold, L.3
  • 37
    • 0029025720 scopus 로고
    • An APL-programmed genetic algorithm for the prediction of RNA secondary structure
    • van Batenburg,F., Gultyaev,A. and Pleij,C. (1995) An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J. Theor. Biol., 174, 269-280.
    • (1995) J. Theor. Biol. , vol.174 , pp. 269-280
    • van Batenburg, F.1    Gultyaev, A.2    Pleij, C.3
  • 38
    • 0022423674 scopus 로고
    • Five pseudoknots are present at the 204 nucleotides long 3′ noncoding region of tobacco mosaic virus RNA
    • van Belkum,A., Abrahams,J., Pleij,C. and Bosch,L. (1985) Five pseudoknots are present at the 204 nucleotides long 3′ noncoding region of tobacco mosaic virus RNA. Nucleic Acids Res., 13, 7673-7686.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 7673-7686
    • van Belkum, A.1    Abrahams, J.2    Pleij, C.3    Bosch, L.4
  • 39
    • 0034554835 scopus 로고    scopus 로고
    • Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA
    • Wuyts,J., Rijk,P.D., de Peer,Y.V., Pison,G., Rousseeuw,P. and Wachter,R.D. (2000) Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res., 28, 4698-4708.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4698-4708
    • Wuyts, J.1    Rijk, P.D.2    de Peer, Y.V.3    Pison, G.4    Rousseeuw, P.5    Wachter, R.D.6
  • 40
    • 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
  • 41
    • 0033562579 scopus 로고    scopus 로고
    • Comparative sequence analysis of tmRNA
    • Zwieb,C., Wower,I. and Wower,J. (1999) Comparative sequence analysis of tmRNA. Nucleic Acids Res., 27, 2063-2071.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2063-2071
    • Zwieb, C.1    Wower, I.2    Wower, J.3


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