RNA Structure Prediction Using Chemical Reaction Optimization

  • Md. Rayhanul KabirEmail author
  • Fatema Tuz Zahra
  • Md. Rafiqul Islam
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 755)


RNA structure prediction (RSP) is an NP-complete problem which has been implemented by various algorithms, e.g., exact and metaheuristics. Here, we have proposed a method to solve RSP problem, which is founded on chemical reaction optimization (CRO), a metaheuristic approach. At first, we have developed a method to generate the solution, and the next four reaction operators of CRO are redesigned and implemented to expand the population all over the solution space. To find the best results from solution space, the values of the fundamental parameters of CRO have assigned accurately. The minimum free energy of RNA structure is computed through INN-HB model to evaluate the fitness of structure. Ten different RNA sequences have been taken for the experiment, and the experimental results of the proposed method are compared with three previous works, RNAPredict, SARNA-Predict, and COIN, to verify the performance of the proposed method.


Chemical reaction optimization RNA structure prediction Ribonucleotide sequences Minimum free energy 


  1. 1.
    Wang, G., Zhang, W., Ning, Q., Chen, H.l.: A novel framework based on ACO and PSO for RNA secondary structure prediction. Math. Probl. Eng. (2013)Google Scholar
  2. 2.
    Mizuno, H., Sundaralingam, M.: Stacking of crick wobble pair and Watson-Crick pair: stability rules of gu pairs at ends of helical stems in trnas and the relation to codon-anticodon wobble interaction. Nucleic Acids Res. 5(11), 4451–4462 (1978)CrossRefGoogle Scholar
  3. 3.
    Neethling, M., Engelbrecht, A.P.: Determining RNA secondary structure using set-based particle swarm optimization. In: IEEE Congress on Evolutionary Computation, 2006. CEC 2006, pp. 1670–1677. IEEE (2006)Google Scholar
  4. 4.
    Zuker, M.: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31(13), 3406–3415 (2003)CrossRefGoogle Scholar
  5. 5.
    McMellan, N.: RNA secondary structure prediction using ant colony optimisation. Master thesis, University of Edinburgh, School of Informatics (2006)Google Scholar
  6. 6.
    Lam, A.Y., Li, V.O.: Chemical reaction optimization for cognitive radio spectrum allocation. In: Global Telecommunications Conference (GLOBECOM 2010), 2010 IEEE, pp. 1–5. IEEE (2010)Google Scholar
  7. 7.
    Lam, A.Y., Li, V.O.: Chemical-reaction-inspired metaheuristic for optimization. IEEE Trans. Evol. Comput. 14(3), 381–399 (2010)CrossRefGoogle Scholar
  8. 8.
    Pan, B., Lam, A.Y., Li, V.O.: Network coding optimization based on chemical reaction optimization. In: Global Telecommunications Conference (GLOBECOM 2011), 2011 IEEE, pp. 1–5. IEEE (2011)Google Scholar
  9. 9.
    Wiese, K.C., Deschenes, A.A., Hendriks, A.G.: Rnapredictan evolutionary algorithm for RNA secondary structure prediction. IEEE/ACM Trans. Comput. Biol. Bioinform. (TCBB) 5(1), 25–41 (2008)CrossRefGoogle Scholar
  10. 10.
    Grypma, P., Tsang, H.H.: SARNA-predict: using adaptive annealing schedule and inversion mutation operator for RNA secondary structure prediction. In: 2014 IEEE Symposium on Computational Intelligence in Multi-Criteria Decision-Making (MCDM), pp. 150–156. IEEE (2014)Google Scholar
  11. 11.
    Srikamdee, S., Wattanapornprom, W., Chongstitvatana, P.: RNA secondary structure prediction with coincidence algorithm. In: 2016 16th International Symposium on Communications and Information Technologies (ISCIT), pp. 686–690. IEEE (2016)Google Scholar
  12. 12.
    Schmitz, M., Steger, G.: Description of RNA folding by “simulated annealing”. J. Mol. Biol. 255(1), 254–266 (1996)CrossRefGoogle Scholar
  13. 13.
    Andronescu, M., Bereg, V., Hoos, H.H., Condon, A.: RNA strand: the RNA secondary structure and statistical analysis database. BMC Bioinform. 9(1), 340 (2008)CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Md. Rayhanul Kabir
    • 1
    Email author
  • Fatema Tuz Zahra
    • 1
  • Md. Rafiqul Islam
    • 1
  1. 1.Computer Science and Engineering DisciplineKhulna UniversityKhulnaBangladesh

Personalised recommendations