Advertisement

A Fast Fuzzy Cocke-Younger-Kasami Algorithm for DNA and RNA Strings Analysis

  • Herón Molina-Lozano
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6438)

Abstract

In this paper we present a variation of the Cocke-Younger-Kasami algorithm (CYK algorithm for short) for the analysis of fuzzy free context languages applied to DNA strings. We propose a variation of the original CYK algorithm where we prove that the order of the new CYK algorithm is O(n). We prove that the new algorithm only use 2n-1 memory localities. We use a variation of the CYK algorithm, where the free context language can be fuzzy. The fuzzy context-free grammar (FCFG) is obtained from DNA and RNA sequences.

Keywords

Pattern recognition Cocke-Younger-Kasami algorithm fuzzy logic ADN RNA 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Lee, E.T., Zadeh, L.A.: Note on Fuzzy Languages. Information Sciences 1, 421–434 (1969)MathSciNetCrossRefGoogle Scholar
  2. 2.
    Asveld, P.R.J.: Fuzzy Context-Free Languages-Part 2: Recognition and Parsing Algorithms. Theoretical Computer Science 347, 191–213 (2005)MathSciNetCrossRefzbMATHGoogle Scholar
  3. 3.
    Molina-Lozano, H., Vallejo-Clemente, E., Morett-Sánchez, J.: DNA Sequence Analysis Using Fuzzy Grammars. IEEE World Congress on Computational Intelligence (2008)Google Scholar
  4. 4.
    Linz, P.: Formal Languages and Automata, 4th edn. Jones and Bartlett Publishers, USA (2006)Google Scholar
  5. 5.
    Hopcroft, J.E., Rajeev Motwai, R., Ullman, J.D.: Introduction to Automata Theory, Languages and Computation. Addison-Wesley, Reading (2002)Google Scholar
  6. 6.
    Duda, R.O., Hart, P.E., Stork, D.G.: Pattern Classification, 2nd edn. Wiley-Interscience, Hoboken (2001)zbMATHGoogle Scholar
  7. 7.
    Searls, D.B.: The Languages of Genes. Nature 420, 211–217 (2002)CrossRefGoogle Scholar
  8. 8.
    Brendel, V., Busse, H.: Genome Structure Described by Formal Languages. Nucleic Acids Research 12, 2561–2568 (1984)CrossRefGoogle Scholar
  9. 9.
    Head, T.: Formal Languages Theory and DNA. Bulleting Mathematical Biology 49 (1987)Google Scholar
  10. 10.
    Searls, D.: The Linguistics of DNA. American Scientific 80, 579–591 (1992)Google Scholar
  11. 11.
    Searls, D.: Artificial Intelligence and Molecular Biology. In: Hunter, L. (ed.) pp. 47–120. AAAI Press, Menlo Park (1993)Google Scholar
  12. 12.
    Collado-Vides, J.: A Transformational Grammar Approach to the Study of the Regulation of Gene Expression. Journal of Theory Biology 136, 403–425 (1989)CrossRefGoogle Scholar
  13. 13.
    Mordeson, J.N., Malik, D.S.: Fuzzy Automata and Languages: Theory and Applications. Chapman and Hall/CRC (2002)Google Scholar
  14. 14.
    Jang, J.-S., Sun, C.-T., Mitzutani, E.: Neuro-Fuzzy and Soft Computing: a Computational Approach to Learning and Machine Intelligence. Prentice-Hall, Englewood Cliffs (1997)Google Scholar
  15. 15.
    Jones, N.C., Pevzner, P.A.: An Introduction to Bioinformatics Algorithms. MIT Press, Cambridge (2004)Google Scholar
  16. 16.
    Database of Protein Domains, Families and Functional Sites, http://www.expasy.ch/prosite

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Herón Molina-Lozano
    • 1
  1. 1.Centro de Investigación en Computación, Instituto Politécnico Nacional, Av. Juan de Dios, Bátiz s/n casi esq. Miguel Othón de Mendizábal. Unidad Profesional Adolfo López Mateos, Col. Nueva Industrial Vallejo Delegación Gustavo A. MaderoMéxico D.F.

Personalised recommendations