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Volumn 393-395, Issue , 2012, Pages 955-960

Study of RNA secondary structure prediction algorithms

Author keywords

Comparative sequence method; Minimum free energy model; Pseudoknot; RNA secondary structure prediction

Indexed keywords

COMPARATIVE SEQUENCE METHOD; COMPUTATIONAL MOLECULAR BIOLOGY; DEVELOPMENT DIRECTIONS; EXISTING PROBLEMS; MATHEMATIC MODEL; MINIMUM FREE ENERGIES; PSEUDOKNOT; RNA SECONDARY STRUCTURE PREDICTION; RNA SECONDARY STRUCTURES;

EID: 84455175171     PISSN: 10226680     EISSN: None     Source Type: Book Series    
DOI: 10.4028/www.scientific.net/AMR.393-395.955     Document Type: Conference Paper
Times cited : (3)

References (29)
  • 2
    • 84455201314 scopus 로고    scopus 로고
    • Beijing: Science Press
    • MOUNT D W. Bioinformatics [M ]. Beijing: Science Press, 2003: 210-228
    • (2003) Bioinformatics [M] , pp. 210-228
    • Mount, D.W.1
  • 3
    • 0033591465 scopus 로고    scopus 로고
    • Expand sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure [J]
    • David H Mathews, Jeffret Sabina, Michael Zuker, Douglas H Turner. Expand sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure [J]. Journal of Molecular Biology, 1999, 288 (5): 911-940
    • (1999) Journal of Molecular Biology , vol.288 , Issue.5 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 4
    • 0031730497 scopus 로고    scopus 로고
    • An RNA folding method capable of identifying pseudoknots and base triples[J]
    • J E Tabaska, RB Cary, HN Gabow, GD Stormo. An RNA folding method capable of identifying pseudoknots and base triples[J]. Bioinformatics,1998,14 (8): 691-699
    • (1998) Bioinformatics , vol.14 , Issue.8 , pp. 691-699
    • Tabaska, J.E.1    Cary, R.B.2    Gabow, H.N.3    Stormo, G.D.4
  • 5
    • 33846900179 scopus 로고    scopus 로고
    • High sensitivity RNA pseudoknot prediction[J]
    • Xiaolu Huang, Hesham Ali. High sensitivity RNA pseudoknot prediction[J]. Nucleic Acids Research, 2007, 35 (2) : 656-663
    • (2007) Nucleic Acids Research , vol.35 , Issue.2 , pp. 656-663
    • Huang, X.1    Ali, H.2
  • 6
    • 24144456561 scopus 로고    scopus 로고
    • A heuristic approach for detecting RNA H-type pseudoknots[J]
    • Huang Chun Hsiang, Lu Chin Lung, Chiu Hsien Tai. A heuristic approach for detecting RNA H-type pseudoknots[J]. Bioinformatics, 2005, 21 (17): 3501-3508
    • (2005) Bioinformatics , vol.21 , Issue.17 , pp. 3501-3508
    • Huang, C.H.1    Lu, C.L.2    Chiu, H.T.3
  • 7
    • 0015216137 scopus 로고
    • Estimation of secondary structure in ribonucleic acids [J]
    • Tinoco I, Uhlenbeck O C,Levine M D. Estimation of secondary structure in ribonucleic acids [J]. Nature,1971 ,230 (5293) :362-367
    • (1971) Nature , vol.230 , Issue.5293 , pp. 362-367
    • Tinoco, I.1    Uhlenbeck, O.C.2    Levine, M.D.3
  • 8
    • 3342977915 scopus 로고    scopus 로고
    • Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization [J]
    • Mathews David H. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization [J]. RNA, 2004, 10(8): 1178-1190
    • (2004) RNA , vol.10 , Issue.8 , pp. 1178-1190
    • Mathews, D.H.1
  • 9
    • 67650536451 scopus 로고    scopus 로고
    • A local-stem-search algorithm to predict the RNA secondary structure[J]
    • CHEN Xiang, BU Dong-Bo, ZHANG Fa, GAO Wen.A Local-stem-search Algorithm to Predict The RNA Secondary Structure[J], Progress in Biochemistry and Biophysics, 2009, 36(1): 115∼121
    • (2009) Progress in Biochemistry and Biophysics , vol.36 , Issue.1 , pp. 115-121
    • Chen, X.1    Bu, D.-B.2    Zhang, F.3    Gao, W.4
  • 10
    • 75549088409 scopus 로고    scopus 로고
    • NNDB: The nearest neighbor parameter database for predicting seability of nucleic acid secondary structure[J]
    • Turner Douglas H, Mathews David H. NNDB: the nearest neighbor parameter database for predicting seability of nucleic acid secondary structure[J]. Nucleic Acids Reaearch, 2010, 38: D280-282
    • (2010) Nucleic Acids Reaearch , vol.38
    • Turner, D.H.1    Mathews, D.H.2
  • 12
    • 0028593508 scopus 로고
    • St ochast ic context - Free grammars for tRNA modeling[J]
    • Sakakibara Y, Brown M, Hughey R, et al. St ochast ic context - free grammars for tRNA modeling[J]. Nucleic Acids Research, 1994, 22: 5112-5120
    • (1994) Nucleic Acids Research , vol.22 , pp. 5112-5120
    • Sakakibara, Y.1    Brown, M.2    Hughey, R.3
  • 14
    • 0032796501 scopus 로고    scopus 로고
    • RNA secondary structure predict ion using stochasti c cont ext- free grammars and evolut ionary history[J]
    • Knudsen B, Hein J. RNA secondary structure predict ion using stochasti c cont ext- free grammars and evolut ionary history[J]. Bioinformatics, 1999, 15: 446-454
    • (1999) Bioinformatics , vol.15 , pp. 446-454
    • Knudsen, B.1    Hein, J.2
  • 15
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure predict ion using stochast ic context - Free grammars [J]
    • Knudsen B, Hein J. Pfold: RNA secondary structure predict ion using stochast ic context - free grammars [J]. Nucleic Acids Research, 2003, 13: 3423-3428
    • (2003) Nucleic Acids Research , vol.13 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 16
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    • Ruan J, Stormo G D, Zhang W. An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics, 2004, 20(1): 58∼66
    • (2004) Bioinformatics , vol.20 , Issue.1 , pp. 58-66
    • Ruan, J.1    Stormo, G.D.2    Zhang, W.3
  • 17
    • 0035991766 scopus 로고    scopus 로고
    • Combinatorial properties of RNA secondary structures
    • Nebel M.E.Combinatorial properties of RNA secondary structures,J Comput Biol.,2002;9: 541-73
    • (2002) J Comput Biol. , vol.9 , pp. 541-573
    • Nebel, M.E.1
  • 18
    • 0031730618 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure based on helical regions distribution[J]
    • Li W.J.,Wu J.J.Prediction of RNA Secondary Structure Based on Helical Regions Distribution[J], Bioinformatics,1998;14:700-706
    • (1998) Bioinformatics , vol.14 , pp. 700-706
    • Li, W.J.1    Wu, J.J.2
  • 19
    • 0029025720 scopus 로고
    • An APL-programmed genetic algorithm for the prediction of RNA secondary structure
    • Van Bantenburg F.H.D.,Gultyaev A.P.,et al.An APL-programmed Genetic Algorithm for the Prediction of RNA Secondary Structure,J.theor.Biol.,1995;174: 269-280
    • (1995) J.theor.Biol. , vol.174 , pp. 269-280
    • Van Bantenburg, F.H.D.1    Gultyaev, A.P.2
  • 20
    • 84455204510 scopus 로고    scopus 로고
    • Application of genetic algorithm in the prediction of RNA secondary structure[J]
    • CAO Su-bing et al. Application of Genetic Algorithm in the Prediction of RNA Secondary Structure[J]. Journal of Anhui Agriculture Science. 2010, 38( 24) : 12933-12934
    • (2010) Journal of Anhui Agriculture Science. , vol.38 , Issue.24 , pp. 12933-12934
    • Cao, S.-B.1
  • 21
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the Prediction of RNA secondary structures with pseudoknots[J]
    • Ruan, J., G. Stormo and W. Zhang. An iterated loop matching approach to the Prediction of RNA secondary structures with pseudoknots[J]. Bioinformatics, 2004(20):58-66
    • (2004) Bioinformatics , vol.20 , pp. 58-66
    • Ruan, J.1    Stormo, G.2    Zhang, W.3
  • 22
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure Prediction using stochastic context-free grammars[J]
    • Knudsen, B. and J. Hein. Pfold: RNA secondary structure Prediction using stochastic context-free grammars[J]. Nucleic Acids Research, 2003(31):3423-3428
    • (2003) Nucleic Acids Research , Issue.31 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 23
    • 0043123155 scopus 로고    scopus 로고
    • Pfold :RNA secondary structure prediction using stochastic context2free grammars [J]
    • Knudsen B ,Hein J. Pfold :RNA secondary structure prediction using stochastic context2free grammars [J]. Nucleic Acids Research ,2003 ,31 (13) :3423-3428.
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 26
    • 24044519380 scopus 로고    scopus 로고
    • MARNA:multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons [J]
    • Siebert, S.and R.Backofen. MARNA:multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons [J]. Bioinformatics, 2005(21):3352-3359
    • (2005) Bioinformatics , Issue.21 , pp. 3352-3359
    • Siebert, S.1    Backofen, R.2
  • 27
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protosequence problems [J]
    • Sankoff D. Simultaneous solution of the RNA folding, alignment and protosequence problems [J]. SIAM Journal on Applied Mathematics ,1985 ,45 (5) :810-825.
    • (1985) SIAM Journal on Applied Mathematics , vol.45 , Issue.5 , pp. 810-825
    • Sankoff, D.1
  • 28
    • 5044242515 scopus 로고    scopus 로고
    • Alignment of RNA base pairing probability matrices [J]
    • Hofacker IL ,Bernhart S, Stadler P. Alignment of RNA base pairing probability matrices [J]. Bioinformatics ,2004 ,20 (14) : 2222-2227.
    • (2004) Bioinformatics , vol.20 , Issue.14 , pp. 2222-2227
    • Hofacker, I.L.1    Bernhart, S.2    Stadler, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.