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Work supported by the Academy of Finland, project 11281; the reader interested in details concerning the unpublished papers is encouraged to contact one of the authors.
Preview
Unable to display preview. Download preview PDF.
References
L. M. Adleman, Molecular computation of solutions to combinatorial problems, Science, 226 (Nov. 1994), 1021–1024.
E. Csuhaj-Varju, J. Dassow, J. Kelemen, Gh. Păun, Grammar Systems. A Grammatical Approach to Distribution and Cooperation, Gordon and Breach, London, 1994.
E. Csuhaj-Varju, L. Kari, Gh. Päun, Test tube distributed systems based on splicing, Computers and AI, 15, 2-3 (1996), 211–232.
E. Csuhaj-Varju, J. Kelemen, Gh. Păun, Grammar systems with WAVE-like communication, Computers and AI, 15, 5 (1996), 419–436.
K. Culik II, T. Harju, Splicing semigroups of dominoes and DNA, Discrete Appl. Math., 31 (1991), 261–277.
J. Dassow, V. Mitrana, Splicing grammar systems, Computers and AI, 15, 2-3, (1996), 109–122.
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.
R. Freund, Gh. Păun, G. Rozenberg, Bidirectional sticker systems, submitted, 1996.
T. Head, Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors, Bull. Math. Biology, 49 (1987), 737–759.
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.
L. Kari, Gh. Păun, G. Rozenberg, A. Salomaa, S. Yu, DNA computing, sticker systems, and universality, submitted, 1996.
L. Kasi, Gh. Păun, G. Thierrin, S. Yu, Characterizing RE using insertion-deletion systems, submitted, 1996.
C. Martin-Vide, Gh. Păun, A. Salomaa, Characterizations of recursively enumerable languages by means of insertion grammars, submitted, 1996.
Gh. Păun, Splicing. A challenge to formal language theorists, Bulletin EATCS, 57 (1995), 183–194.
Gh. Păun, On the power of splicing grammar systems, Ann. Univ. Buc., Matem.Inform. Series, 45, 1 (1996), 93–106.
Gh. Păun, Regular extended H systems are computationally universal, J. Aut., Languages, Combinatorics, 1, 1 (1996), 27–36.
Gh. Păun, Universal DNA computing models based on the splicing operation, Second Annual Meeting on DNA Based Computers, Princeton, 1996, 67–86.
Gh. Păun, Splicing systems with targets are computationally universal, Inform. Processing Letters, 59 (1996), 129–133.
Gh. Păun, On the splicing operation, Discrete Applied Math., 70 (1996), 57–79.
Gh. Păun, Contextual Grammars. From, Natural Languages to Formal Languages and Back, forthcoming (1997).
Gh. Păun, G. Rozenberg, Sticker systems, submitted, 1997.
Gh. Păun, G. Rozenberg, A. Salomaa, Computing by splicing, Theor. Computer Sci., 168, 2 (1996), 321–336.
Gh. Păun, A. Salomaa, DNA computing based on the splicing operation, Mathematica Japonica, 43, 3 (1996), 607–632.
Gh. Păun, L. Săntean (now Kari), Parallel communicating grammar systems: the regular case, Ann. Univ. Buc., Matem.-Inform. Series, 38 (1989), 55–63.
D. Pixton, Regularity of splicing languages, Discrete Appl. Math., 69 (1996), 101–124.
A. Salomaa, Jewels of Formal Language Theory, Computer Science Press, Rockwille, Maryland, 1981.
W. Smith, A., Schweitzer, DNA computers in vitro and in vivo, manuscript in circulation, March 1995.
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.
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 1997 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
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
Download citation
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