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German Conference on Bioinformatics

GCB 1996: Bioinformatics pp 210–220Cite as

From DNA recombination to DNA computing via formal languages

  • Formal Languages and DNA
  • Conference paper
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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1278))

Abstract

We briefly present notions and results from three directions of research which use formal language theory tools for modelling operations specific to DNA (and RNA) recombinations; in all cases one obtains computability models which are universal (language generating devices are obtained which are equivalent in power with Turing machines). The basic operations are those of sticking (a model of the Watson-Crick complementarity), of splicing (a model of the recombinant behaviour of DNA sequences under the influence of restriction enzymes), and of insertion/deletion (known to hold both for DNA and for RNA sequences). Because this paper is an overview, we present here only definitions and results without proofs; further details can be found in the papers quoted below.

Work supported by the Academy of Finland, project 11281; the reader interested in details concerning the unpublished papers is encouraged to contact one of the authors.

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References

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

    Google Scholar 

  2. E. Csuhaj-Varju, J. Dassow, J. Kelemen, Gh. Păun, Grammar Systems. A Grammatical Approach to Distribution and Cooperation, Gordon and Breach, London, 1994.

    Google Scholar 

  3. E. Csuhaj-Varju, L. Kari, Gh. Päun, Test tube distributed systems based on splicing, Computers and AI, 15, 2-3 (1996), 211–232.

    Google Scholar 

  4. E. Csuhaj-Varju, J. Kelemen, Gh. Păun, Grammar systems with WAVE-like communication, Computers and AI, 15, 5 (1996), 419–436.

    Google Scholar 

  5. K. Culik II, T. Harju, Splicing semigroups of dominoes and DNA, Discrete Appl. Math., 31 (1991), 261–277.

    Article  Google Scholar 

  6. J. Dassow, V. Mitrana, Splicing grammar systems, Computers and AI, 15, 2-3, (1996), 109–122.

    Google Scholar 

  7. R. Freund, L. Kari, Gh. Păun, DNA computing based on splicing: The existence of universal computers, Technical Report 185-2/FR-2/95, TU Wien, 1995.

    Google Scholar 

  8. R. Freund, Gh. Păun, G. Rozenberg, Bidirectional sticker systems, submitted, 1996.

    Google Scholar 

  9. T. Head, Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors, Bull. Math. Biology, 49 (1987), 737–759.

    Article  Google Scholar 

  10. T. Head, Gh. Păun, D. Pixton, Language theory and molecular genetics. Generative mechanisms suggested by DNA recombination, in Handbook of Formal Languages (G. Rozenberg, A. Salomaa, eds.), Springer-Verlag, Berlin, Heidelberg, 1996.

    Google Scholar 

  11. L. Kari, Gh. Păun, G. Rozenberg, A. Salomaa, S. Yu, DNA computing, sticker systems, and universality, submitted, 1996.

    Google Scholar 

  12. L. Kasi, Gh. Păun, G. Thierrin, S. Yu, Characterizing RE using insertion-deletion systems, submitted, 1996.

    Google Scholar 

  13. C. Martin-Vide, Gh. Păun, A. Salomaa, Characterizations of recursively enumerable languages by means of insertion grammars, submitted, 1996.

    Google Scholar 

  14. Gh. Păun, Splicing. A challenge to formal language theorists, Bulletin EATCS, 57 (1995), 183–194.

    Google Scholar 

  15. Gh. Păun, On the power of splicing grammar systems, Ann. Univ. Buc., Matem.Inform. Series, 45, 1 (1996), 93–106.

    Google Scholar 

  16. Gh. Păun, Regular extended H systems are computationally universal, J. Aut., Languages, Combinatorics, 1, 1 (1996), 27–36.

    Google Scholar 

  17. Gh. Păun, Universal DNA computing models based on the splicing operation, Second Annual Meeting on DNA Based Computers, Princeton, 1996, 67–86.

    Google Scholar 

  18. Gh. Păun, Splicing systems with targets are computationally universal, Inform. Processing Letters, 59 (1996), 129–133.

    Article  Google Scholar 

  19. Gh. Păun, On the splicing operation, Discrete Applied Math., 70 (1996), 57–79.

    Article  Google Scholar 

  20. Gh. Păun, Contextual Grammars. From, Natural Languages to Formal Languages and Back, forthcoming (1997).

    Google Scholar 

  21. Gh. Păun, G. Rozenberg, Sticker systems, submitted, 1997.

    Google Scholar 

  22. Gh. Păun, G. Rozenberg, A. Salomaa, Computing by splicing, Theor. Computer Sci., 168, 2 (1996), 321–336.

    Article  Google Scholar 

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

    Google Scholar 

  24. Gh. Păun, L. Săntean (now Kari), Parallel communicating grammar systems: the regular case, Ann. Univ. Buc., Matem.-Inform. Series, 38 (1989), 55–63.

    Google Scholar 

  25. D. Pixton, Regularity of splicing languages, Discrete Appl. Math., 69 (1996), 101–124.

    Article  Google Scholar 

  26. A. Salomaa, Jewels of Formal Language Theory, Computer Science Press, Rockwille, Maryland, 1981.

    Google Scholar 

  27. W. Smith, A., Schweitzer, DNA computers in vitro and in vivo, manuscript in circulation, March 1995.

    Google Scholar 

  28. Cl. Zandrou, Cl Ferretti, G. Mauri, A reduced distributed splicing system for RE languages, in Control, Cooperation, Combinatorics. New Trends in Formal Languages (Gh. Păun, A. Salomaa, eds.), Springer-Verlag, Heidelberg, 1997, 319–329.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Institute of Mathematics of the Romanian Academy, PO Box 1 - 764, 70700, Bucureşti, Romania

    Gheorghe Păun

  2. Department of Mathematics, Academy of Finland and University of Turku, 20500, Turku, Finland

    Arto Salomaa

Authors
  1. Gheorghe Păun
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  2. Arto Salomaa
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Editor information

Ralf Hofestädt Thomas Lengauer Markus Löffler Dietmar Schomburg

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© 1997 Springer-Verlag Berlin Heidelberg

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Păun, G., Salomaa, A. (1997). From DNA recombination to DNA computing via formal languages. In: Hofestädt, R., Lengauer, T., Löffler, M., Schomburg, D. (eds) Bioinformatics. GCB 1996. Lecture Notes in Computer Science, vol 1278. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0033219

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  • DOI: https://doi.org/10.1007/BFb0033219

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-63370-9

  • Online ISBN: 978-3-540-69524-0

  • eBook Packages: Springer Book Archive

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