메뉴 건너뛰기




Volumn 21, Issue 17, 2005, Pages 3501-3508

A heuristic approach for detecting RNA H-type pseudoknots

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE FUNCTION; INFORMATION PROCESSING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; STRUCTURAL BIOINFORMATICS; STRUCTURE ANALYSIS;

EID: 24144456561     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti568     Document Type: Article
Times cited : (44)

References (39)
  • 1
    • 0025315854 scopus 로고
    • Prediction of RNA secondary structure, including pseudoknotting, by computer simulation
    • Abrahams,J.P. et al. (1990) Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res. 18, 3035-3044.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 3035-3044
    • Abrahams, J.P.1
  • 2
    • 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 Applied Mathematics 104, 45-62.
    • (2000) Discrete Applied Mathematics , vol.104 , pp. 45-62
    • Akutsu, T.1
  • 3
    • 0030310297 scopus 로고    scopus 로고
    • RNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search
    • (Hunter,L. and Klein,T., eds)
    • Brown,M. and Wilson,C. (1996) RNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search. In Proceedings of the 1996 Pacific Symposium on Biocomputing, (Hunter,L. and Klein,T., eds), pp. 109-125.
    • (1996) Proceedings of the 1996 Pacific Symposium on Biocomputing , pp. 109-125
    • Brown, M.1    Wilson, C.2
  • 4
    • 3543069105 scopus 로고    scopus 로고
    • Stochastic modeling of RNA pseudoknotted structures: A grammatical approach
    • Cai,L. et al. (2003) Stochastic modeling of RNA pseudoknotted structures: A grammatical approach. Bioinformatics, 19, 66-73.
    • (2003) Bioinformatics , vol.19 , pp. 66-73
    • Cai, L.1
  • 5
    • 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.J. 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.J.1
  • 7
    • 0043285072 scopus 로고    scopus 로고
    • A partition function algorithm for nucleic acid secondary structure including pseudoknots
    • Dirks,R.M. and Pierce,N.A. (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem., 24, 1664-1677.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1664-1677
    • Dirks, R.M.1    Pierce, N.A.2
  • 8
    • 0025878210 scopus 로고
    • The computer simulation of RNA folding involving pseudoknot formation
    • Gultyaev,A.P. (1991) The computer simulation of RNA folding involving pseudoknot formation. Nucleic Acids Res., 19, 2489-2494.
    • (1991) Nucleic Acids Res. , vol.19 , pp. 2489-2494
    • Gultyaev, A.P.1
  • 9
    • 0029061125 scopus 로고
    • The computer simulation o f RNA folding pathways using a genetic algorithm
    • Gultyaev,A.P. et al. (1995) The computer simulation o f RNA folding pathways using a genetic algorithm. J. Mol. Biol., 250 37-51.
    • (1995) J. Mol. Biol. , vol.250 , pp. 37-51
    • Gultyaev, A.P.1
  • 10
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker,I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 11
    • 0027112854 scopus 로고
    • An efficient algorithm for finding a maximum weight 2-independent set on interval graphs
    • Hsiao,J.Y. et al. (1992) An efficient algorithm for finding a maximum weight 2-independent set on interval graphs. Information Processing Letters, 43, 229-235.
    • (1992) Information Processing Letters , vol.43 , pp. 229-235
    • Hsiao, J.Y.1
  • 12
    • 0742286998 scopus 로고    scopus 로고
    • Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs
    • Ieong,S. et al. (2003) Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs. J. Comput. Biol., 10, 981-995.
    • (2003) J. Comput. Biol. , vol.10 , pp. 981-995
    • Ieong, S.1
  • 13
    • 0032540504 scopus 로고    scopus 로고
    • NMR structure of a classical pseudoknot: Interplay of single-and double-stranded RNA
    • Kolk,M.H. et al. (1998) NMR structure of a classical pseudoknot: interplay of single-and double-stranded RNA. Science, 280, 434-438.
    • (1998) Science , vol.280 , pp. 434-438
    • Kolk, M.H.1
  • 14
    • 0033709625 scopus 로고    scopus 로고
    • RNA pseudoknot prediction in energy-based models
    • Lyngsø,R.B. and Pedersen,C.N. (2000) RNA pseudoknot prediction in energy-based models. J. Comput. Biol., 7, 409-427.
    • (2000) J. Comput. Biol. , vol.7 , pp. 409-427
    • Lyngsø, R.B.1    Pedersen, C.N.2
  • 15
    • 0035890840 scopus 로고    scopus 로고
    • RNAMotif, an RNA secondary structure definition and search algorithm
    • Macke,T.J. et al. (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res., 29, 4724-4735.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 4724-4735
    • Macke, T.J.1
  • 16
    • 0024278647 scopus 로고
    • Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA
    • McPheeters,D.S. et al. (1988) Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA. J. Mol. Biol., 201, 517-535.
    • (1988) J. Mol. Biol. , vol.201 , pp. 517-535
    • McPheeters, D.S.1
  • 17
    • 0036893436 scopus 로고    scopus 로고
    • Terminal RNA replication elements in human parechovirus 1
    • Nateri,A.S. et al. (2002) Terminal RNA replication elements in human parechovirus 1. J. Virol., 76, 13116-13122.
    • (2002) J. Virol. , vol.76 , pp. 13116-13122
    • Nateri, A.S.1
  • 18
    • 0025351085 scopus 로고
    • Pseudoknots: A new motif in the RNA game
    • Pleij,C.W. (1990) Pseudoknots: A new motif in the RNA game. TIBS, 15, 143-147.
    • (1990) TIBS , vol.15 , pp. 143-147
    • Pleij, C.W.1
  • 19
    • 0024836211 scopus 로고
    • RNA pseudoknots: Structure, detection, and prediction
    • Pleij,C.W. and Bosch,L. (1989) RNA pseudoknots: Structure, detection, and prediction. Methods Enzymol., 180, 289-303.
    • (1989) Methods Enzymol. , vol.180 , pp. 289-303
    • Pleij, C.W.1    Bosch, L.2
  • 21
    • 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
  • 22
    • 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. et al. (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
  • 23
    • 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
  • 24
    • 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
  • 25
    • 0035105948 scopus 로고    scopus 로고
    • The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation
    • Shapiro,B.A. et al. (2001) The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation. Bioinformatics, 17, 137-148.
    • (2001) Bioinformatics , vol.17 , pp. 137-148
    • Shapiro, B.A.1
  • 26
    • 0030774724 scopus 로고    scopus 로고
    • Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm
    • Shapiro,B.S. and Wu,J.C. (1997) Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm. CABIOS, 13, 459-471.
    • (1997) CABIOS , vol.13 , pp. 459-471
    • Shapiro, B.S.1    Wu, J.C.2
  • 27
    • 0031730497 scopus 로고    scopus 로고
    • An RNA folding method capable of identifying pseudoknots and base triples
    • Tabaska,J.E. et al. (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.E.1
  • 29
    • 0026483177 scopus 로고
    • Structural and functional aspects of RNA pseudoknots
    • ten Dam,E.B. et al. (1992) Structural and functional aspects of RNA pseudoknots. Biochemistry, 31, 11665-11676.
    • (1992) Biochemistry , vol.31 , pp. 11665-11676
    • ten Dam, E.B.1
  • 30
    • 5044241491 scopus 로고    scopus 로고
    • MuSiC: A tool for multiple sequence alignment with constraints
    • Tsai,Y.T. et al. (2004) MuSiC: A tool for multiple sequence alignment with constraints. Bioinformatics, 20, 2309-2311.
    • (2004) Bioinformatics , vol.20 , pp. 2309-2311
    • Tsai, Y.T.1
  • 31
    • 0026651981 scopus 로고
    • RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase
    • Tuerk,C. et al. (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
  • 32
    • 0029025720 scopus 로고
    • An APL-programmed genetic algorithm for the prediction of RNA secondary structure
    • van Batenburg,F.H. et al. (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.H.1
  • 33
    • 0035170790 scopus 로고    scopus 로고
    • PseudoBase: Structural information on RNA pseudoknots
    • van Batenburg,F.H. et al. (2001) PseudoBase: Structural information on RNA pseudoknots. Nucleic Acids Res., 29, 194-195.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 194-195
    • van Batenburg, F.H.1
  • 34
    • 0033954144 scopus 로고    scopus 로고
    • PseudoBase: A database with RNA pseudoknots
    • van Batenburg,F.H. et al. (2000) PseudoBase: A database with RNA pseudoknots. Nucleic Acids Res., 28, 201-204.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 201-204
    • van Batenburg, F.H.1
  • 35
    • 0022423674 scopus 로고
    • Five pseudoknots are present at the 204 nucleotides long 3′ noncoding region of tobacco mosaic virus RNA
    • van Belkum,A. et al. (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
  • 36
    • 0032827591 scopus 로고    scopus 로고
    • A phylogenetically conserved hairpin-type 39 untranslated region pseudoknot functions in coronavirus RNA replication
    • Williams,G.D. et al. (1999) A phylogenetically conserved hairpin-type 39 untranslated region pseudoknot functions in coronavirus RNA replication. J. Virol., 73, 8349-8355.
    • (1999) J. Virol. , vol.73 , pp. 8349-8355
    • Williams, G.D.1
  • 37
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406 3415.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 38
    • 0000616205 scopus 로고
    • RNA secondary structure and their prediction
    • Zuker,M. and Sankoff,D. (1984) RNA secondary structure and their prediction. Bull. Math. Biol., 46, 591-621.
    • (1984) Bull. Math. Biol. , vol.46 , pp. 591-621
    • Zuker, M.1    Sankoff, D.2
  • 39
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.