Comparison of HSRNAFold and RNAFold algorithms for RNA secondary structure prediction

IEEE Region 10 Annual International Conference, Proceedings/TENCON

Volumn , Issue , 2009, Pages

  Mohsen, Abdulqader M ^a   Khader, Ahamad Tajudin ^a   Ramachandram, Dhanesh ^a  

^a SCHOOL OF PHYSICS   (Malaysia)

Author keywords

Dynamic programming algorithms; Meta heuristic algorithms; Minimum free energy; Rna folding

Indexed keywords

COMPLEX OPTIMIZATION; COMPUTATIONAL PREDICTIONS; DYNAMIC PROGRAMMING ALGORITHM; DYNAMIC PROGRAMMING TECHNIQUES; HARMONY SEARCH; HARMONY SEARCH ALGORITHMS; META HEURISTIC ALGORITHM; MINIMUM FREE ENERGIES; PHYSICAL METHODS; PROTEIN SYNTHESIS; RIBONUCLEIC ACID; RNA FOLDING; RNA SECONDARY STRUCTURE PREDICTION; RNA SECONDARY STRUCTURES; RNA STRUCTURES; STRUCTURE DETERMINATION; TEST SEQUENCE;

DYNAMIC PROGRAMMING; FORECASTING; FREE ENERGY; LEARNING ALGORITHMS; RNA;

HEURISTIC ALGORITHMS;

EID: 77951140500     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/TENCON.2009.5395933     Document Type: Conference Paper

References (13)

1. J. A. Doudna and T. R. Cech, "The chemical repertoire of natural ribozymes," Nature, vol.418, no.6894, pp. 222-228, 2002.
2. J. L. Hansen, T. M. Schmeing, P. B. Moore, and T. A. Steitz, "Structural insights into peptide bond formation," in Proceedings of the National Academy of Sciences, vol.99, 2002, pp. 11 670-11 675.
3. J. Bachellerie, J. Cavaill, and A. Httenhofer, "The expanding snorna world," Biochimie, vol.84, no.8, pp. 775-790(16), August 2002.
4. H. Tsang and K. Wiese, "Sarna-predict: A study of rna secondary structure prediction using different annealing schedules," in Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2007, pp. 239-246.
5. M. Neethling and A. Engelbrecht, "Determining rna secondary structure using set-based particle swarm optimization," in IEEE Congress on Evolutionary Computation(CEC2006), 2006, pp. 1670-1677. (Pubitemid 47130698)
6. A. A. Deschenes, "A genetic algorithm for rna secondary structure prediction using stacking energy thermodyamic models," Ph.D. dissertation, Simon Fraser University, 2005.
7. 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.
8. M. Zuker, "Mfold web server for nucleic acid folding and hybridization prediction," Nucleic Acids Research, vol.31, no.13, p. 34063415, 2003.
9. I. Hofacker, W. Fontana, P. Stadler, S. Bonhoeffer, M. Tacker, and P. Schuster, "Fast folding and comparison of rna secondary structures (the vienna rna package)," Monatshefte f. Chemie, vol.125, pp. 167-188, 1994.
10. H. H. Tsang, "Sarna-predict: A permutation-based simulated annealing algorithm for rna secondary structure prediction," Ph.D. dissertation, Simon Fraser University, 2007.
11. K. Wiese, A. Deschnes, and A. Hendriks, "Rnapredict - an evolutionary algorithm for rna secondary structure prediction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.5, no.1, pp. 25-41, 2007.
12. A. Hendriks, "A parallel evolutionary algorithm for rna secondary structure prediction," Ph.D. dissertation, Simon Fraser University, May2005.
13. 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.