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Volumn 38, Issue SUPPL. 2, 2010, Pages

CyloFold: Secondary structure prediction including pseudoknots

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 77954288431     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq432     Document Type: Article
Times cited : (48)

References (24)
  • 3
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (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.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 4
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews,D.H., Disney,M.D., Childs,J.L., Schroeder,S.J., Zuker,M. and Turner,D.H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.L.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 5
    • 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
  • 6
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • Rivas,E. and Eddy,S.R. (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.R.2
  • 7
    • 34547564982 scopus 로고    scopus 로고
    • pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
    • Reeder,J., Steffen,P. and Giegerich,R. (2007) pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. Nucleic Acids Res., 35, W320-W324.
    • (2007) Nucleic Acids Res. , vol.35
    • Reeder, J.1    Steffen, P.2    Giegerich, R.3
  • 8
    • 75649099055 scopus 로고    scopus 로고
    • Improved free energy parameters for RNA pseudoknotted secondary structure prediction
    • Andronescu,M.S., Pop,C. and Condon,A.E. (2010) Improved free energy parameters for RNA pseudoknotted secondary structure prediction. RNA, 16, 26-42.
    • (2010) RNA , vol.16 , pp. 26-42
    • Andronescu, M.S.1    Pop, C.2    Condon, A.E.3
  • 9
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    • 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, 58-66.
    • (2004) Bioinformatics , vol.20 , pp. 58-66
    • Ruan, J.1    Stormo, G.D.2    Zhang, W.3
  • 10
    • 0030774724 scopus 로고    scopus 로고
    • Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm
    • Shapiro,B.A. and Wu,J.C. (1997) Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm. Comput. Appl. Biosci., 13, 459-471.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 459-471
    • Shapiro, B.A.1    Wu, J.C.2
  • 11
    • 0035823067 scopus 로고    scopus 로고
    • RNA folding pathway functional intermediates: their prediction and analysis
    • Shapiro,B.A., Bengali,D., Kasprzak,W. and Wu,J.C. (2001) RNA folding pathway functional intermediates: their prediction and analysis. J Mol Biol, 312, 27-44.
    • (2001) J Mol Biol , vol.312 , pp. 27-44
    • Shapiro, B.A.1    Bengali, D.2    Kasprzak, W.3    Wu, J.C.4
  • 12
    • 0029040124 scopus 로고
    • A genetic algorithm to search for optimal and suboptimal RNA secondary structures
    • Benedetti,G. and Morosetti,S. (1995) A genetic algorithm to search for optimal and suboptimal RNA secondary structures. Biophys. Chem., 55, 253-259.
    • (1995) Biophys. Chem. , vol.55 , pp. 253-259
    • Benedetti, G.1    Morosetti, S.2
  • 13
    • 0029061125 scopus 로고
    • The computer simulation of RNA folding pathways using a genetic algorithm
    • Gultyaev,A.P., van Batenburg,F.H. and Pleij,C.W. (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.P.1    van Batenburg, F.H.2    Pleij, C.W.3
  • 14
    • 0028547954 scopus 로고
    • A massively parallel genetic algorithm for RNA secondary structure prediction
    • Shapiro,B.A. and Navetta,J. (1994) A massively parallel genetic algorithm for RNA secondary structure prediction. J. Supercomput., 8, 195-207.
    • (1994) J. Supercomput. , vol.8 , pp. 195-207
    • Shapiro, B.A.1    Navetta, J.2
  • 15
    • 33750505657 scopus 로고    scopus 로고
    • Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm
    • Shapiro,B.A., Kasprzak,W., Grunewald,C. and Aman,J. (2006) Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm. J. Mol. Graph Model, 25, 514-531.
    • (2006) J. Mol. Graph Model , vol.25 , pp. 514-531
    • Shapiro, B.A.1    Kasprzak, W.2    Grunewald, C.3    Aman, J.4
  • 16
    • 0035105948 scopus 로고    scopus 로고
    • The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation
    • Shapiro,B.A., Wu,J.C., Bengali,D. and Potts,M.J. (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    Wu, J.C.2    Bengali, D.3    Potts, M.J.4
  • 17
    • 25844447772 scopus 로고    scopus 로고
    • HotKnots: heuristic prediction of RNA secondary structures including pseudoknots
    • Ren,J., Rastegari,B., Condon,A. and Hoos,H.H. (2005) HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11, 1494-1504.
    • (2005) RNA , vol.11 , pp. 1494-1504
    • Ren, J.1    Rastegari, B.2    Condon, A.3    Hoos, H.H.4
  • 19
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: interactive drawing and editing of the RNA secondary structure
    • Darty,K., Denise,A. and Ponty,Y. (2009) VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975.
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3
  • 23
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: software for nucleic acid folding and hybridization
    • Markham,N.R. and Zuker,M. (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol., 453, 3-31.
    • (2008) Methods Mol. Biol. , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 24
    • 0021760032 scopus 로고
    • An RNA folding rule
    • Martinez,H.M. (1984) An RNA folding rule. Nucleic Acids Res., 12, 323-334.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 323-334
    • Martinez, H.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.