Recombinant DNA ,Gene Splicing as Generative Devices of Formal Languages

  • Paola Bonizzoni
  • Clelia De Felice
  • Giancarlo Mauri
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3526)


Recombinant DNA


Formal Language Regular Language Generative Device Formal Language Theory Splice System 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Berstel, J., Perrin, D.: Theory of Codes. Academic Press, New York (1985)zbMATHGoogle Scholar
  2. 2.
    Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: Linear splicing and syntactic monoid (2004) (submitted)Google Scholar
  3. 3.
    Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: Decision problems on linear and circular splicing. In: Ito, M., Toyama, M. (eds.) DLT 2002. LNCS, vol. 2450, pp. 78–92. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  4. 4.
    Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: Regular languages generated by reflexive finite linear splicing systems. In: Ésik, Z., Fülöp, Z. (eds.) DLT 2003. LNCS, vol. 2710, pp. 134–145. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  5. 5.
    Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: DNA and circular splicing. In: Condon, A., Rozenberg, G. (eds.) DNA 2000. LNCS, vol. 2054, pp. 117–129. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  6. 6.
    Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: Circular splicing and regularity. Theoretical Informatics and Appl. 38, 189–228 (2004)zbMATHCrossRefMathSciNetGoogle Scholar
  7. 7.
    Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: On the power of circular splicing (2004) (submitted)Google Scholar
  8. 8.
    Bonizzoni, P., De Felice, C., Zizza, R.: The structure of reflexive regular splicing languages via Schützenberger constants. Theoretical Computer Science (2004) (to appear)Google Scholar
  9. 9.
    Bonizzoni, P., Ferretti, C., Mauri, G., Zizza, R.: Separating some splicing models. Information Processing Letters 76(6), 255–259 (2001)CrossRefMathSciNetGoogle Scholar
  10. 10.
    Bonizzoni, P., Mauri, G.: Regular splicing languages and subclasses. Theoretical Computer Science (2004) (to appear)Google Scholar
  11. 11.
    Culik, K., Harju, T.: Splicing semigroups of dominoes and DNA. Discrete Applied Math. 31, 261–277 (1991)zbMATHCrossRefMathSciNetGoogle Scholar
  12. 12.
    Fagnot, I.: Splicing Systems and Chomsky hierarchy. In: Proc. of Journees Montoises 2004, Lieges, Belgium (2004)Google Scholar
  13. 13.
    Laun, E.G.: Constants and splicing systems, PHD Thesis, Binghamton University (1999)Google Scholar
  14. 14.
    Goode, E., Pixton, D.: Recognizing splicing languages: syntactic monoids and simultaneous pumping (2004) (submitted), available from
  15. 15.
    Head, T.: Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviours. Bull. Math. Biol. 49, 737–759 (1987)zbMATHMathSciNetGoogle Scholar
  16. 16.
    Head, T.: Splicing languages generated with one sided context. In: Paun, G. (ed.) Computing with bio-molecules: theory and experiments. Springer, Heidelberg (1998)Google Scholar
  17. 17.
    Head, T., Paun, G., Pixton, D.: Language theory and molecular genetics: generative mechanisms suggested by DNA recombination. In: Rozenberg, G., Salomaa, A. (eds.) Handbook of Formal Languages, vol. 2, pp. 295–360. Springer, Heidelberg (1996)Google Scholar
  18. 18.
    Harrison, M.A.: Introduction to Formal Language Theory. Addison-Wesley, Reading (1978)zbMATHGoogle Scholar
  19. 19.
    Hopcroft, J.E., Motwani, R., Ullman, J.D.: Introduction to Automata Theory, Languages, and Computation. Addison-Wesley, Reading (2001)zbMATHGoogle Scholar
  20. 20.
    Kim, S.M.: An algorithm for identifying spliced languages. In: Jiang, T., Lee, D.T. (eds.) COCOON 1997. LNCS, vol. 1276, pp. 403–411. Springer, Heidelberg (1997)CrossRefGoogle Scholar
  21. 21.
    Kim, S.M.: Computational modeling for genetic splicing systems. SIAM Journal of Computing 26, 1284–1309 (1997)zbMATHCrossRefGoogle Scholar
  22. 22.
    McNaughton, R., Papert, S.: Counter-Free Automata. MIT Press, Cambridge (1971)zbMATHGoogle Scholar
  23. 23.
    Paun, G.: On the splicing operation. Discrete Applied Math. 70, 57–79 (1996)zbMATHCrossRefMathSciNetGoogle Scholar
  24. 24.
    Paun, G., Rozenberg, G., Salomaa, A.: DNA computing, New Computing Paradigms. Springer, Heidelberg (1998)zbMATHGoogle Scholar
  25. 25.
    Perrin, D.: Finite Automata. In: Van Leeuwen, J. (ed.) Handbook of Theoretical Computer Science, vol. B, pp. 1–57. Elsevier, Amsterdam (1990)Google Scholar
  26. 26.
    Pixton, D.: Linear and circular splicing systems. In: Proc. of 1st Int. Symp. on Intelligence in Neural and Biological Systems, pp. 181–188. IEEE Computer Society Press, Los Alamitos (1996), Silver SpringGoogle Scholar
  27. 27.
    Pixton, D.: Regularity of splicing languages. Discrete Applied Math. 69, 101–124 (1996)zbMATHCrossRefMathSciNetGoogle Scholar
  28. 28.
    Schützenberger, M.P.: Sur certaines opérations de fermeture dans les langages rationnels. Symposia Mathematica 15, 245–253 (1975)Google Scholar
  29. 29.
    Verlan, S., Zizza, R.: 1–splicing vs. 2–splicing: separating results. In: Proc. of Words 2003, Turku, Finland, pp. 320–331 (2003)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Paola Bonizzoni
    • 1
  • Clelia De Felice
    • 2
  • Giancarlo Mauri
    • 1
  1. 1.Dipartimento di Informatica Sistemistica e ComunicazioneUniversitá degli Studi di Milano BicoccaMilanoItaly
  2. 2.Dipartimento di Informatica ed ApplicazioniUniversitá di SalernoBaronissi (SA)Italy

Personalised recommendations