Solution to Motif Finding Problem in Membranes

  • Katrina B. Gapuz
  • Ephraim D. Mendoza
  • Richelle Ann B. Juayong
  • Nestine Hope S. Hernandez
  • Francis George C. Cabarle
  • Henry N. Adorna
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10105)

Abstract

The study of genes is an important field of biology. A way to understand genetic composition is through finding regularly occurring nucleotide sequences, or motifs, in a DNA sequence. However, finding these motifs is difficult and is shown to be NP-complete. In this paper, we use a variant of P systems called Evolution-Communication P systems with Energy using string objects to solve the Motif Finding Problem in O(lt)-time where l is the length of the motif and t is the number of DNA sequences given.

Keywords

Membrane computing Evolution-communication P systems with energy Motif finding 

References

  1. 1.
    Adorna, H., Păun, G., Pérez-Jiménez, M.J.: On communication complexity in evolution-communication P systems. Roman. J. Inf. Sci. Technol. 13, 113–130 (2010)Google Scholar
  2. 2.
    Ausiello, G., Crescenzi, P., Gambosi, G., Kann, V., Marchetti-Spaccamela, A., Protasi, M.: Complexity and Approximation: Combinatorial Optimization Problems and Their Approximability Properties, 1st edn. Springer, Heidelberg (1999)CrossRefMATHGoogle Scholar
  3. 3.
    Cavaliere, M.: Evolution–communication P systems. In: PĂun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.) WMC 2002. LNCS, vol. 2597, pp. 134–145. Springer, Heidelberg (2003). doi:10.1007/3-540-36490-0_10 CrossRefGoogle Scholar
  4. 4.
    Fontana, F., Franco, G.: Finding the maximum element using P systems. J. Univ. Comput. Sci. 10(5), 567–580 (2004)MathSciNetGoogle Scholar
  5. 5.
    Gapuz, K., Mendoza, E., Juayong, R.A., Hernandez, N.H., Adorna, H.: Solution to a restricted motif finding problem in membranes. In: Sioson, A., et al. (eds.) Proceedings of the 16th Philippine Computing Science Congress (PCSC 2016), pp. 136–147. Puerto Princesa, Palawan (2016). https://sites.google.com/site/2016pcsc/proceedings Google Scholar
  6. 6.
    Jones, N., Pevzner, P.: An Introduction to Bioinformatics Algorithms. Massachusetts Institute of Technology Press, Cambridge (2004)Google Scholar
  7. 7.
    Leavitt, S.A.: Deciphering the Genetic Code. https://history.nih.gov/exhibits/nirenberg/glossary.htm. Accessed 20 Feb 2016
  8. 8.
    Naranayan, K.S.: Language of P systems; computability and complexity. Master’s thesis, Indian Institute of Technology Madras (2001)Google Scholar
  9. 9.
    Păun, G.: Membrane Computing. Springer, Heidelberg (2002)CrossRefMATHGoogle Scholar
  10. 10.
    Păun, G.: Introduction to Membrane Computing. In: Ciobanu, G., Păun, G., Pérez-Jiménez, M.J. (eds.) Applications of Membrane Computing. Natural Computing Series, pp. 1–42. Springer, Heidelberg (2006). http://dx.doi.org/10.1007/3-540-29937-8_1 Google Scholar
  11. 11.
    Pérez–Jiménez, M.J.: A computational complexity theory in membrane computing. In: Păun, G., Pérez-Jiménez, M.J., Riscos-Núñez, A., Rozenberg, G., Salomaa, A. (eds.) WMC 2009. LNCS, vol. 5957, pp. 125–148. Springer, Heidelberg (2010). doi:10.1007/978-3-642-11467-0_10 CrossRefGoogle Scholar
  12. 12.
    Sipser, M.: Introduction to the Theory of Computation, 2nd edn. Thomson Course Technology, San Francisco (2006)MATHGoogle Scholar
  13. 13.
    Zeng, X., Zhang, X., Zou, Q.: Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks. Brief. Bioinform. 17(2), 193–203 (2016)CrossRefGoogle Scholar
  14. 14.
    Zou, Q., Li, J., Song, L., Zeng, X., Wang, G.: Similarity computation strategies in the microRNA-disease network: a survey. Brief. Funct. Genomics 15(1), 55–64 (2016)Google Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Katrina B. Gapuz
    • 1
  • Ephraim D. Mendoza
    • 1
  • Richelle Ann B. Juayong
    • 1
  • Nestine Hope S. Hernandez
    • 1
  • Francis George C. Cabarle
    • 1
  • Henry N. Adorna
    • 1
  1. 1.Algorithms and Complexity Lab, Department of Computer ScienceUniversity of the Philippines DilimanQuezon CityPhilippines

Personalised recommendations