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Decision Problems for Linear and Circular Splicing Systems

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Developments in Language Theory (DLT 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2450))

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Abstract

We will consider here the splicing systems, generative devices inspired by cut and paste phenomena on DNA molecules under the action of restriction and ligase enzymes. A DNA strand can be viewed as a string over a four letter alphabet (the four deoxyribonucleotides), therefore we can model DNA computation within the framework of formal language theory. In spite of a vast literature on splicing systems, briefly surveyed here, a few problems related to their computational power are still open. We intend to evidence how classical techniques and concepts in automata theory are a legitimate tool for investigating some of these problems.

Partially supported by MIUR Project “Linguaggi Formali e Automi: teoria ed applicazioni” and by the contribution of EU Commission under The Fifth Framework Programme, project MolCoNet IST-2001-32008.

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References

  1. Adleman, L. M.: Molecular computation of solutions to combinatorial problems. Science 226 (1994) 1021–1024

    Article  Google Scholar 

  2. Berstel, J., Perrin, D.: Theory of codes. Academic Press, New York (1985)

    MATH  Google Scholar 

  3. Berstel, J., Restivo, A.: Codes et sousmonoides fermes par conjugaison. Sem. LITP 81–45 (1981) 10 pages

    Google Scholar 

  4. Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: DNA and circular splicing. In: Condon, A., Rozenberg, G. (eds.): DNA Computing. Lecture Notes in Computer Science, Vol. 2054. Springer-Verlag, New York (2001) 117–129

    Chapter  Google Scholar 

  5. Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: Circular splicing and regularity (2002) submitted

    Google Scholar 

  6. Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: On the power of linear and circular splicing (2002) submitted

    Google Scholar 

  7. Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: The structure of regular reflexive splicing languages via Schützenberger constants (2002) manuscript

    Google Scholar 

  8. Bonizzoni, P., Ferretti, C., Mauri, G.: Splicing systems with marked rules. Romanian Journal of Information Science and Technology 1:4 (1998) 295–306

    Google Scholar 

  9. Bonizzoni, P., Ferretti, C., Mauri, G., Zizza, R.: Separating some splicing models. Information Processing Letters 76:6 (2001) 255–259

    Article  MathSciNet  Google Scholar 

  10. Choffrut, C., Karhumaki, J.: Combinatorics onWords. In: Rozenberg, G., Salomaa, A., (eds.): Handbook of Formal Languages, Vol. 1. Springer-Verlag, (1996) 329–438

    Google Scholar 

  11. Culik, K., Harju, T.: Splicing semigroups of dominoes and DNA. Discrete Applied Mathematics 31 (1991) 261–277

    Article  MATH  MathSciNet  Google Scholar 

  12. De Luca, A., Restivo, A.: A characterization of strictly locally testable languages and its application to subsemigroups. Information and Control 44 (1980) 300–319

    Article  MATH  MathSciNet  Google Scholar 

  13. Denningho., K.L., Gatterdam, R.W.: On the undecidability of splicing systems. International Journal of Computer Math. 27 (1989) 133–145

    Article  Google Scholar 

  14. Freund, R., Kari, L., Paun, Gh.: DNA Computing based on splicing. The existence of universal computers. Theory of Computing Systems 32 (1999) 69–112

    Article  MATH  MathSciNet  Google Scholar 

  15. Gatterdam, R.W.: Algorithms for splicing systems. SIAM Journal of Computing21:3 (1992) 507–520

    Article  MATH  MathSciNet  Google Scholar 

  16. Goode, E., Head, T., Pixton D.: private communication

    Google Scholar 

  17. Goode, E., Pixton, D.: Semi-simple splicing systems. In: Martin-Vide, C., Mitrana, V. (eds.): Where Mathematics, Computer Science, Linguistics and Biology Meet. Kluwer Academic Publ., Dordrecht (2001) 343–357

    Google Scholar 

  18. Head, T.: Splicing schemes and DNA. In: Lindenmayer Systems. Impacts on Theoretical Computer Science and Developmental Biology. Springer-Verlag, Berlin (1992) 371–383

    Google Scholar 

  19. Head, T.: Formal Language Theory and DNA. An analysis of the generative capacity of specific recombinant behaviours. Bull. Math. Biol. 49 (1987) 737–759

    MATH  MathSciNet  Google Scholar 

  20. Head, T.: Splicing languages generated with one sided context. In: Paun, Gh. (ed.): Computing with Bio-molecules. Theory and Experiments, Springer-Verlag Singapore (1998)

    Google Scholar 

  21. Head, T.: Splicing representations of strictly locally testable languages. Discrete Applied Math. 87 (1998) 139–147

    Article  MATH  MathSciNet  Google Scholar 

  22. Head, T.: Circular suggestions for DNA Computing. In: Carbone, A., Gromov, M., Pruzinkiewicz, P. (eds.): Pattern Formation in Biology, Vision and Dynamics. World Scientific, Singapore and London, to appear

    Google Scholar 

  23. Head, T.: Splicing systems. Regular languages and below. In: Pre-Proc. of DNA8 (2002)

    Google Scholar 

  24. Head, T., Paun, Gh., 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. Springer-Verlag (1996) 295–360

    Google Scholar 

  25. Head, T., Rozenberg, G., Bladergroen, R., Breek, C., Lommerse, P., Spaink, H.: Computing with DNA by operating on plasmids. BioSystems 57 (2000) 87–93

    Article  Google Scholar 

  26. Hopcroft, J.E., Motwani, R., Ullman, J.D.: Introduction to Automata Theory, Languages, and Computation. 2nd edn. Addison-Wesley, Reading, Mass. (2001)

    MATH  Google Scholar 

  27. Jonoska, N., Karl, S.: A molecular computation of the road coloring problem. In: Proc. of 2nd Annual Meeting on DNA Based Computers. DIMACS Workshop (1996) 148–158

    Google Scholar 

  28. Kari, L.: DNA computing. An arrival of biological mathematics. The Mathematical Intelligence 19:2 (1999) 9–22

    MathSciNet  Google Scholar 

  29. Kim, S.M.: An Algorithm for Identifying Spliced Languages. In: Proc. of Cocoon97. Lecture Notes in Computer Science, Vol. 1276. Springer-Verlag (1997) 403–411

    Google Scholar 

  30. Kim, S.M.: Computational modeling for genetic splicing systems. SIAM Journal of Computing 26 (1997) 1284–1309

    Article  MATH  Google Scholar 

  31. Lothaire, M.: Combinatorics on Words. Encyclopedia of Math. and its Applications. Addison Wesley Publishing Company (1983)

    Google Scholar 

  32. McNaughton, R., Papert, S.: Counter-Free Automata. MIT Press, Cambridge, Mass. (1971)

    Google Scholar 

  33. Mateescu, A., Paun, Gh., Rozenberg, G., Salomaa, A.: Simple splicing systems. Discrete Applied Mathematics 84 (1998) 145–163

    Article  MATH  MathSciNet  Google Scholar 

  34. Paun, Gh.: On the splicing operation. Discrete Applied Mathematics 70 (1996) 57–79

    Article  MATH  MathSciNet  Google Scholar 

  35. Paun, Gh.: Regular extended H systems are computationally universal. Journal of Automata, Languages and Combinatorics. 1:1 (1996) 27–36

    MATH  MathSciNet  Google Scholar 

  36. Paun, Gh., Salomaa, A.: DNA computing based on the splicing operation. Mathematica Japonica 43:3 (1996) 607–632

    MATH  MathSciNet  Google Scholar 

  37. Paun, Gh., Rozenberg, G., Salomaa, A.: Computing by splicing. Theoretical Computer Science 168:2 (1996) 321–336

    Article  MATH  MathSciNet  Google Scholar 

  38. Paun, Gh., Rozenberg, G., Salomaa, A.: DNA computing, New Computing Paradigms. Springer-Verlag (1998)

    Google Scholar 

  39. Perrin, D.: Finite Automata. In: van Leeuwen, J. (ed.): Handbook of Theoretical Computer Science, Vol. B. Elsevier (1990) 1–57

    Google Scholar 

  40. Pixton, D.: Splicing in abstract families of languages. Theoretical Computer Science 234 (2000) 135–166

    Article  MATH  MathSciNet  Google Scholar 

  41. Pixton, D.: Linear and Circular Splicing Systems. In: Proc. of 1st Int. Symp. on Int. in Neural and Biological Systems (1996) 181–188

    Google Scholar 

  42. Pixton, D.: Regularity of splicing languages. Discrete Applied Mathematics 69 (1996) 101–124

    Article  MATH  MathSciNet  Google Scholar 

  43. Reis, C., Thierren, G.: Reflective star languages and codes. Information and Control 42 (1979) 1–9

    Article  MATH  MathSciNet  Google Scholar 

  44. Schützenberger, M.-P.: Sur certaines opérations de fermeture dans le langages rationnels. Symposia Mathematica 15 (1975) 245–253

    Google Scholar 

  45. Siromoney, R.: Distributed Circular Systems. In: Pre-Proc. of Grammar Systems 2000, Austria

    Google Scholar 

  46. Siromoney, R., Subramanian, K.G., Dare, A.: Circular DNA and Splicing Systems. In: Proc. of ICPIA. Lecture Notes in Computer Science, Vol. 654. Springer-Verlag (1992) 260–273

    Google Scholar 

  47. Yokomori, T., Kobayaski, S., Ferretti, C.: On the power of circular splicing systems and DNA computability. In: Proc. of IEEE Int. Conf. Evol. Comp. ICEC99

    Google Scholar 

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Author information

Authors and Affiliations

  1. Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano - Bicocca, Via Bicocca degli Arcimboldi 8, 20126, Milano, Italy

    Paola Bonizzoni & Giancarlo Mauri

  2. Dipartimento di Informatica ed Applicazioni, Università di Salerno, 84081, Baronissi, SA, Italy

    Clelia De Felice & Rosalba Zizza

Authors
  1. Paola Bonizzoni
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  2. Clelia De Felice
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  3. Giancarlo Mauri
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  4. Rosalba Zizza
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Editor information

Editors and Affiliations

  1. Faculty of Science and Faculty of Engineering, Kyoto Sangyo University, 603-8555, Kyoto, Japan

    Masami Ito  & Masafumi Toyama  & 

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Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R. (2003). Decision Problems for Linear and Circular Splicing Systems. In: Ito, M., Toyama, M. (eds) Developments in Language Theory. DLT 2002. Lecture Notes in Computer Science, vol 2450. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45005-X_7

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  • DOI: https://doi.org/10.1007/3-540-45005-X_7

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  • Print ISBN: 978-3-540-40431-6

  • Online ISBN: 978-3-540-45005-4

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