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Volumn 32, Issue , 2009, Pages 923-929

Predicting the minimum free energy RNA secondary structures using harmony search algorithm

Author keywords

Dynamic programming algorithms; Harmony search optimization; Metaheuristic algorithms; Minimum Free Energy; RNA folding

Indexed keywords

DYNAMIC PROGRAMMING ALGORITHM; HARMONY SEARCH; META HEURISTIC ALGORITHM; MINIMUM FREE ENERGIES; RNA FOLDING;

EID: 84871851455     PISSN: 2010376X     EISSN: 20103778     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (2)

References (30)
  • 1
    • 0037062949 scopus 로고    scopus 로고
    • The chemical repertoire of natural ribozymes
    • J. A. Doudna and T. R. Cech, "The chemical repertoire of natural ribozymes, " Nature, vol. 418, no. 6894, pp. 222-228, 2002.
    • (2002) Nature , vol.418 , Issue.6894 , pp. 222-228
    • Doudna, J.A.1    Cech, T.R.2
  • 3
    • 0036703184 scopus 로고    scopus 로고
    • The expanding snorna world
    • (16), August
    • J. Bachellerie, J. Cavaill, and A. Httenhofer, "The expanding snorna world, " Biochimie, vol. 84, no. 8, pp. 775-790(16), August 2002.
    • (2002) Biochimie , vol.84 , Issue.8 , pp. 775-790
    • Bachellerie, J.1    Cavaill, J.2    Httenhofer, A.3
  • 4
    • 4644223259 scopus 로고    scopus 로고
    • Mechanisms of gene silencing by doublestranded rna
    • G. Meister and T. Tuschl, "Mechanisms of gene silencing by doublestranded rna, " Nature, vol. 431, pp. 343-349, 2004.
    • (2004) Nature , vol.431 , pp. 343-349
    • Meister, G.1    Tuschl, T.2
  • 7
    • 13344279384 scopus 로고    scopus 로고
    • Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for rna secondary structure prediction
    • K. J. Doshi, J. J. Cannone, C. W. Cobaugh, and R. R. Gutell, "Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for rna secondary structure prediction, " BMC Bioinformatics, vol. 5, no. 105, pp. 1471-2105, 2004.
    • (2004) BMC Bioinformatics , vol.5 , Issue.105 , pp. 1471-2105
    • Doshi, K.J.1    Cannone, J.J.2    Cobaugh, C.W.3    Gutell, R.R.4
  • 8
    • 33746320475 scopus 로고    scopus 로고
    • Revolutions in rna secondary structure prediction
    • D. H. Mathews, "Revolutions in rna secondary structure prediction, " Journal of Molecular Biology, vol. 359, p. 526532, 2006.
    • (2006) Journal of Molecular Biology , vol.359 , pp. 526532
    • Mathews, D.H.1
  • 10
    • 0019082587 scopus 로고
    • Fast algorithm for predicting the secondary structure of single-stranded rna
    • R. Nussinov and A. Jacobson, "Fast algorithm for predicting the secondary structure of single-stranded rna, " Proc Natl Acad Sci U S A, vol. 77, no. 11, pp. 6309-6313, 1980.
    • (1980) Proc Natl Acad Sci U S A , vol.77 , Issue.11 , pp. 6309-6313
    • Nussinov, R.1    Jacobson, A.2
  • 11
    • 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, " Nucl. Acids. Res, vol. 9, no. 1, pp. 133-148, 1981.
    • (1981) Nucl. Acids. Res , vol.9 , Issue.1 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 12
    • 0028249154 scopus 로고
    • Prediction of rna secondary structure by energy minimization
    • ser. Methods in Molecular Biology, M. G. Annette and G. G. Hugh, Eds. Humana Press, 10.1385/0-89603-276-0:267
    • M. Zuker, "Prediction of rna secondary structure by energy minimization, " in Computer Analysis of Sequence Data, ser. Methods in Molecular Biology, M. G. Annette and G. G. Hugh, Eds. Humana Press, 1994, pp. 267-294, 10.1385/0-89603-276-0:267.
    • (1994) Computer Analysis of Sequence Data , pp. 267-294
    • Zuker, M.1
  • 13
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • M. Zuker, "Mfold web server for nucleic acid folding and hybridization prediction, " Nucleic Acids Research, vol. 31, no. 13, p. 34063415, 2003.
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 34063415
    • Zuker, M.1
  • 15
    • 0032512621 scopus 로고    scopus 로고
    • Dynamic competition between alternative structures in viroid rnas simulated by an rna folding algorithm
    • A. Gultyaev, F. van Batenburg, and C. Pleij, "Dynamic competition between alternative structures in viroid rnas simulated by an rna folding algorithm, " Journal of Molecular Biology, vol. 276, no. 1, pp. 43-55, 1998.
    • (1998) Journal of Molecular Biology , vol.276 , Issue.1 , pp. 43-55
    • Gultyaev, A.1    van Batenburg, F.2    Pleij, C.3
  • 17
    • 33645821671 scopus 로고    scopus 로고
    • Comparison of p-rnapredict and mfold algorithms for rna secondary structure prediction
    • K. C. Wiese and A. Hendriks, "Comparison of p-rnapredict and mfold algorithms for rna secondary structure prediction, " Bioinformatics, vol. 22, no. 8, p. 934942, 2006.
    • (2006) Bioinformatics , vol.22 , Issue.8 , pp. 934942
    • Wiese, K.C.1    Hendriks, A.2
  • 18
    • 79955288861 scopus 로고    scopus 로고
    • The signifcance of thermodynamic models in the accuracy improvement of rna secondary structure prediction using permutation-based simulated annealing
    • Singapore
    • H. Tsang and K. Wiese, "The signifcance of thermodynamic models in the accuracy improvement of rna secondary structure prediction using permutation-based simulated annealing, " in Proceedings of the IEEE Congress on Evolutionary Computation, Singapore, 2007, pp. 3879-3885.
    • (2007) Proceedings of the IEEE Congress on Evolutionary Computation , pp. 3879-3885
    • Tsang, H.1    Wiese, K.2
  • 19
    • 34548781416 scopus 로고    scopus 로고
    • A particle swarm optimizer for finding minimum free energy rna secondary structures
    • SIS 2007, IEEE, 2007
    • M. Geis and M. Middendorf, "A particle swarm optimizer for finding minimum free energy rna secondary structures, " in Swarm Intelligence Symposium, 2007. SIS 2007. IEEE, 2007, pp. 1-8.
    • (2007) Swarm Intelligence Symposium , pp. 1-8
    • Geis, M.1    Middendorf, M.2
  • 21
    • 0034974417 scopus 로고    scopus 로고
    • A new heuristic optimization algorithm: Harmony search
    • Z. W. Geem, J. H. Kim, and G. Loganathan, "A new heuristic optimization algorithm: Harmony search, " SIMULATION, vol. 76, no. 2, pp. 60-68, 2001.
    • (2001) SIMULATION , vol.76 , Issue.2 , pp. 60-68
    • Geem, Z.W.1    Kim, J.H.2    Loganathan, G.3
  • 22
    • 34248141625 scopus 로고    scopus 로고
    • An improved harmony search algorithm for solving optimization problems
    • M. Mahdavi, M. Fesanghary, and E. Damangir, "An improved harmony search algorithm for solving optimization problems, " Applied Mathematics and Computation, vol. 188, no. 2, pp. 1567-1579, 2007.
    • (2007) Applied Mathematics and Computation , vol.188 , Issue.2 , pp. 1567-1579
    • Mahdavi, M.1    Fesanghary, M.2    Damangir, E.3
  • 24
    • 26644439939 scopus 로고    scopus 로고
    • Jviz. rna-a java tool for rna secondary structure visualization
    • K. C. Wiese, E. Glen, and A. Vasudevan, "jviz. rna-a java tool for rna secondary structure visualization, " IEEE Transactions on NanoBioscience, vol. 4, no. 3, pp. 212-218, 2005.
    • (2005) IEEE Transactions on NanoBioscience , vol.4 , Issue.3 , pp. 212-218
    • Wiese, K.C.1    Glen, E.2    Vasudevan, A.3
  • 25
    • 13744249396 scopus 로고    scopus 로고
    • A statistical analysis of rna folding algorithms through thermodynamic parameter perturbation
    • D. M. Layton and R. Bundschuh, "A statistical analysis of rna folding algorithms through thermodynamic parameter perturbation, " Nucleic Acids Research, vol. 33, no. 2, p. 519524, 2005.
    • (2005) Nucleic Acids Research , vol.33 , Issue.2 , pp. 519524
    • Layton, D.M.1    Bundschuh, R.2
  • 27
    • 77953136145 scopus 로고    scopus 로고
    • Chaotic harmony search algorithms
    • [Online]. Available
    • B. Alatas, "Chaotic harmony search algorithms, " Applied Mathematics and Computation, vol. 216, no. 9, pp. 2687-2699, 2010. [Online]. Available: http://www.sciencedirect.com/science/article/B6TY8-4YPPPWP-6/2/489c124258d50da8d1930a2be60e777a
    • (2010) Applied Mathematics and Computation , vol.216 , Issue.9 , pp. 2687-2699
    • Alatas, B.1
  • 28
    • 20444466485 scopus 로고    scopus 로고
    • A new meta-heuristic algorithm for continuous engineering optimization: Harmony search theory and practice
    • K. S. Lee and Z. W. Geem, "A new meta-heuristic algorithm for continuous engineering optimization: harmony search theory and practice, " Computer Methods in Applied Mechanics and Engineering, vol. 194, no. 36-38, pp. 3902-3933, 2005.
    • (2005) Computer Methods in Applied Mechanics and Engineering , vol.194 , Issue.36-38 , pp. 3902-3933
    • Lee, K.S.1    Geem, Z.W.2
  • 29
    • 84871906569 scopus 로고    scopus 로고
    • Harmony search in water pump switching problem
    • Z. W. Geem, "Harmony search in water pump switching problem, " ICNC, vol. 3, pp. Pp 751-760, 2005.
    • (2005) ICNC , vol.3 , pp. 751-760
    • Geem, Z.W.1
  • 30
    • 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
    • M. L. V, M. K. M, P. N, Y. N. Shang Z, and G. R. R
    • J. J. Cannone, S. Subramanian, M. N. Schnare, J. R. Collett, L. D'Souza, L. N. Du Y, Feng B, M. L. V, M. K. M, P. N, Y. N. Shang Z, and G. R.R., "The comparative rna web (crw) site: an online database of comparative sequence and structure information for ribosomal, intron, and other rnas, " BMC Bioinformatics, vol. 3, no. 35, pp. 169-172, 2002.
    • (2002) BMC Bioinformatics , vol.3 , Issue.35 , pp. 169-172
    • Cannone, J.J.1    Subramanian, S.2    Schnare, M.N.3    Collett, J.R.4    D'Souza, L.5    Du, Y.L.N.6    Feng, B.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.