메뉴 건너뛰기




Volumn 4175 LNBI, Issue , 2006, Pages 262-273

Rapid ab initio RNA folding including pseudoknots via graph tree decomposition

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL COMPLEXITY; CONFORMATIONS; DATA STRUCTURES; GRAPH THEORY; HEURISTIC METHODS; MOLECULAR STRUCTURE;

EID: 33750258941     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11851561_25     Document Type: Conference Paper
Times cited : (14)

References (25)
  • 1
    • 0025315854 scopus 로고
    • Prediction of RNA secondary structure, including pseudoknotting, by computer simulation
    • J. Abrahams, M. van den Berg, E. van Batenburg, and C. Pleij. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res., 18:3035-3044, 1990.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 3035-3044
    • Abrahams, J.1    Van Den Berg, M.2    Van Batenburg, E.3    Pleij, C.4
  • 3
    • 0000964917 scopus 로고
    • Dynamic programming algorithms on graphs with bounded tree-width
    • Springer Verlag, Lecture Notes in Computer Science
    • H. L. Bodlaender. Dynamic programming algorithms on graphs with bounded tree-width. In Proc. 15th Int'l Colloquium on Automata, Languages and Programming ICALP'87, pages 105-119. Springer Verlag, Lecture Notes in Computer Science, vol. 317, 1987.
    • (1987) Proc. 15th Int'l Colloquium on Automata, Languages and Programming ICALP'87 , vol.317 , pp. 105-119
    • Bodlaender, H.L.1
  • 4
    • 0344298926 scopus 로고    scopus 로고
    • The ribonuclease p database
    • J. Brown. The ribonuclease p database. Nucleic Acids Res., 27:314, 1999.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 314
    • Brown, J.1
  • 5
    • 0034651542 scopus 로고    scopus 로고
    • Prediction of common secondary structures of RNAs: A genetic algorithm approach
    • J.-H. Chen, S.-Y. Le, and J.V. Maize. Prediction of common secondary structures of RNAs: a genetic algorithm approach. Nucleic Acids Research, 28(4):991-999, 2000.
    • (2000) Nucleic Acids Research , vol.28 , Issue.4 , pp. 991-999
    • Chen, J.-H.1    Le, S.-Y.2    Maize, J.V.3
  • 6
    • 0043285072 scopus 로고    scopus 로고
    • A partition function algorithm for nucleic acid secondary structure including pseudoknots
    • R. Dirks and N. Pierce. A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem., 24:16641677, 2003.
    • (2003) J. Comput. Chem. , vol.24 , pp. 16641677
    • Dirks, R.1    Pierce, N.2
  • 8
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • S.R. Eddy and R. Durbin. RNA sequence analysis using covariance models. Nucleic Acids Research, 22:2079-2088, 1994.
    • (1994) Nucleic Acids Research , vol.22 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 9
    • 0034724565 scopus 로고    scopus 로고
    • Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frame shifting
    • D. Giedroc, C. Theimer, and P. Nixon. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frame shifting. J. of Molecular Biology, 298:167-185, 2000.
    • (2000) J. of Molecular Biology , vol.298 , pp. 167-185
    • Giedroc, D.1    Theimer, C.2    Nixon, P.3
  • 11
    • 3543051100 scopus 로고    scopus 로고
    • A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences
    • Y. Ji, X. Xu, and G.D. Stormo. A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics, 20(10):1591-1602, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.10 , pp. 1591-1602
    • Ji, Y.1    Xu, X.2    Stormo, G.D.3
  • 12
    • 2442641641 scopus 로고    scopus 로고
    • A conformational switch controls hepatitis delta virus ribozyme catalysis
    • A. Ke, K. Zhou, F. Ding, J.H. Gate, and J.A. Doudna. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature, 429:201205, 2004.
    • (2004) Nature , vol.429 , pp. 201205
    • Ke, A.1    Zhou, K.2    Ding, F.3    Gate, J.H.4    Doudna, J.A.5
  • 13
    • 0033709625 scopus 로고    scopus 로고
    • RNA pseudoknot prediction in energy-based models
    • R.B. Lyngso and C.N.S. Pedersen. RNA pseudoknot prediction in energy-based models. J. of Computational Biology, 7(3-4):409-427, 2000.
    • (2000) J. of Computational Biology , vol.7 , Issue.3-4 , pp. 409-427
    • Lyngso, R.B.1    Pedersen, C.N.S.2
  • 14
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of the thermodynamic parameters improves prediction of RNA secondary structure
    • D.H. Mathews, J. Sabina, M. Zuker, and C.N.S. Pederson. Expanded sequence dependence of the thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288:911-940, 1999.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Pederson, C.N.S.4
  • 16
    • 25844447772 scopus 로고    scopus 로고
    • HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots
    • J. Ren, B. Rastegart, A. Condon, and H.H. Hoos. HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11:1194-1504, 2005.
    • (2005) RNA , vol.11 , pp. 1194-1504
    • Ren, J.1    Rastegart, B.2    Condon, A.3    Hoos, H.H.4
  • 17
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • E. Rivas and S.R. Eddy. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Molecular Biology, 285:2053-2068, 1999.
    • (1999) J. Molecular Biology , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 18
    • 0000673493 scopus 로고
    • Graph minors ii. algorithmic aspects of tree width
    • N. Robertson and P.D. Seymour. Graph minors ii. algorithmic aspects of tree width. J. Algorithms, 7:309-322, 1986.
    • (1986) J. Algorithms , vol.7 , pp. 309-322
    • Robertson, N.1    Seymour, P.D.2
  • 19
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    • J. Ruan, G.D. Stormo, and W. Zhang. An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics, 20(1):58-66, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.1 , pp. 58-66
    • Ruan, J.1    Stormo, G.D.2    Zhang, W.3
  • 20
    • 0029100233 scopus 로고
    • Predicting thermodynamic properties of RNA
    • M.J. Serra, D.H. Turner, and S.M. Freier. Predicting thermodynamic properties of RNA. Meth. Enzymol., 259:243-261, 1995.
    • (1995) Meth. Enzymol. , vol.259 , pp. 243-261
    • Serra, M.J.1    Turner, D.H.2    Freier, S.M.3
  • 21
    • 33745492418 scopus 로고    scopus 로고
    • Tree decomposition based fast search of RNA structures including pseudoknots in genomes
    • IEEE Computer Society
    • Y. Song, C. Liu, R. L. Malmberg, F. Pan, and L. Cai, Tree decomposition based fast search of RNA structures including pseudoknots in genomes. In Proc. Comput. System Bioinformatics Coraf. CSB'05, pages 223-234. IEEE Computer Society, 2005.
    • (2005) Proc. Comput. System Bioinformatics Coraf. CSB'05 , pp. 223-234
    • Song, Y.1    Liu, C.2    Malmberg, R.L.3    Pan, F.4    Cai, L.5
  • 23
    • 0031730497 scopus 로고    scopus 로고
    • An RNA folding method capable of identifying pseudoknots and base triples
    • J. Tabaska, R. Cary, H. Gabow, and G. Stormo. An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics, 14(8):691-699, 1998.
    • (1998) Bioinformatics , vol.14 , Issue.8 , pp. 691-699
    • Tabaska, J.1    Cary, R.2    Gabow, H.3    Stormo, G.4
  • 25
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • M. Zuker and P. Stiegler. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9(1):133-148, 1981.
    • (1981) Nucleic Acids Res. , vol.9 , Issue.1 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.