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DNA and circular splicing?

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DNA Computing (DNA 2000)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2054))

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Abstract

Circular splicing has been very recently introduced to model a specific recombinant behaviour of circular DNA, carrying on the investigation initiated with linear splicing. In this paper we restrict ourselves to the relationship between circular regular languages and circular splicing languages. We provide partial results towards a characterization of the class of circular regular languages generated by finite circular splicing systems. We consider a class of languages X* closed under conjugacy relation and with X a regular languages, called here star languages. Using automata theory and combinatorial techniques on words, we show that for a subclass of star languages the corresponding circular languages are circular (Paun) splicing languages. In particular, star languages with X being a finite set or X* being a free monoid belong to this subclass.

Partially supported by MURST Project “Unconventional Computational Models: Syntactic and Combinatorial Methods” — “Modelli di calcolo innovativi: Metodi sintattici e combinatori”.

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References

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

    Article  Google Scholar 

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

    MATH  Google Scholar 

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

    Google Scholar 

  4. P. Bonizzoni, R. Zizza, Deciding whether a regular language is a splicing language, submitted, (1999).

    Google Scholar 

  5. P. Bonizzoni, C. De Felice, G. Mauri, R. Zizza, Circular splicing and regular languages, manuscript, (2000).

    Google Scholar 

  6. P. Bonizzoni, C. De Felice, G. Mauri, R. Zizza, Linear and circular splicing, WORDS99, (1999).

    Google Scholar 

  7. P. Bonizzoni, C. Ferretti, G. Mauri, R. Zizza, Separating some splicing models, Grammar Systems 2000, (2000).

    Google Scholar 

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

    Article  MATH  MathSciNet  Google Scholar 

  9. R. W. Gatterdam, Algorithms for splicing systems, SIAM Journal of Computing, 21:3, (1992), 507–520.

    Article  MATH  MathSciNet  Google Scholar 

  10. D. Giammarresi, A. Restivo, Two-dimensional Languages, in: Handbook of Formal Languages, G. Rozenberg & A. Salomaa, Eds., Springer Verlag, Vol. 3, (1996), 215–267.

    Google Scholar 

  11. T. Head, Formal Language Theory and DNA: an analysis of the generative capacity of specific recombinant behaviors, Bull. Math. Biol., 49, No. 5, (1987), 737–759.

    MATH  MathSciNet  Google Scholar 

  12. T. Head, Gh. Paun, 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, Vol. 2, (1996), 295–360.

    Google Scholar 

  13. J.E. Hopcroft, J.D. Ullman, Introduction to Automata Theory, Languages, and Computing, Addison-Wesley, Reading, Mass. (1979).

    Google Scholar 

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

    Article  MATH  Google Scholar 

  15. M. Lothaire, Combinatorics on Words, Encyclopedia of Math. and its Appl., Addison Wesley Publishing Company (1983).

    Google Scholar 

  16. G. Paun, On the splicing operation, Discrete Applied Math., 70, (1996), 57–79.

    Article  MATH  MathSciNet  Google Scholar 

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

    Google Scholar 

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

    Article  MATH  MathSciNet  Google Scholar 

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

    Article  MATH  MathSciNet  Google Scholar 

  20. R. Siromoney, K.G. Subramanian, A. Dare, Circular DNA and Splicing Systems, Proc. of ICPIA, LNCS 654, Springer-Verlag, (1992), 260–273.

    Google Scholar 

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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 & Rosalba Zizza

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

    Clelia De Felice

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. Department of Computer Science, University of British Columbia, 201-2366 Main Mall, Vancouver, B.C., Canada, V6T 1Z4

    Anne Condon

  2. Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, 2333 CA, Leiden, The Netherlands

    Grzegorz Rozenberg

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© 2001 Springer-Verlag Berlin Heidelberg

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Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R. (2001). DNA and circular splicing?. In: Condon, A., Rozenberg, G. (eds) DNA Computing. DNA 2000. Lecture Notes in Computer Science, vol 2054. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44992-2_9

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  • DOI: https://doi.org/10.1007/3-540-44992-2_9

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42076-7

  • Online ISBN: 978-3-540-44992-8

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