Decision problems for linear and circular splicing systems

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2450, Issue , 2003, Pages 78-92

  Bonizzoni, Paola ^a   De Felice, Clelia ^b   Mauri, Giancarlo ^a   Zizza, Rosalba ^b  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b UNIVERSITY OF SALERNO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

CLASSICAL TECHNIQUES; COMPUTATIONAL POWER; CUT-AND-PASTE; DECISION PROBLEMS; DEOXYRIBONUCLEOTIDES; DNA COMPUTATION; DNA MOLECULES; SPLICING SYSTEMS;

COMPUTATION THEORY;

EID: 84949813419     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-45005-x_7     Document Type: Conference Paper

References (47)

1. Adleman, L. M.: Molecular computation of solutions to combinatorial problems. Science 226 (1994) 1021 − 1024
2. Berstel, J., Perrin, D.: Theory of codes. Academic Press, New York (1985)
3. Berstel, J., Restivo, A.: Codes et sousmonoides fermes par conjugaison. Sem. LITP 81-45 (1981) 10 pages
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
5. Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: Circular splicing and regularity (2002) submitted
6. Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: On the power of linear and circular splicing (2002) submitted
7. Bonizzoni, P., De Felice, C., Mauri, G., Zizza, R.: The structure of regular reflexive splicing languages via Schützenberger constants (2002) manuscript
8. Bonizzoni, P., Ferretti, C., Mauri, G.: Splicing systems with marked rules. Romanian Journal of Information Science and Technology 1:4 (1998) 295 − 306
9. Bonizzoni, P., Ferretti, C., Mauri, G., Zizza, R.: Separating some splicing models. Information Processing Letters 76:6 (2001) 255 − 259
10. Choffrut, C., Karhumaki, J.: Combinatorics onWords. In: Rozenberg, G., Salomaa, A., (eds.): Handbook of Formal Languages, Vol. 1. Springer-Verlag, (1996) 329−438
11. Culik, K., Harju, T.: Splicing semigroups of dominoes and DNA. Discrete Applied Mathematics 31 (1991) 261 − 277
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
13. Denninghoff, K.L., Gatterdam, R.W.: On the undecidability of splicing systems. International Journal of Computer Math. 27 (1989) 133 − 145
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
15. Gatterdam, R.W.: Algorithms for splicing systems. SIAM Journal of Computing 21:3 (1992) 507 − 520
16. Goode, E., Head, T., Pixton D.: private communication
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
18. Head, T.: Splicing schemes and DNA. In: Lindenmayer Systems. Impacts on Theoretical Computer Science and Developmental Biology. Springer-Verlag, Berlin (1992) 371 − 383
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
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)
21. Head, T.: Splicing representations of strictly locally testable languages. Discrete Applied Math. 87 (1998) 139 − 147
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
23. Head, T.: Splicing systems. Regular languages and below. In: Pre-Proc. of DNA 8 (2002)
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
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
26. Hopcroft, J.E., Motwani, R., Ullman, J.D.: Introduction to Automata Theory, Languages, and Computation. 2nd edn. Addison-Wesley, Reading, Mass. (2001)
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
28. Kari, L.: DNA computing. An arrival of biological mathematics. The Mathematical Intelligence 19:2 (1999) 9 − 22
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
30. Kim, S.M.: Computational modeling for genetic splicing systems. SIAM Journal of Computing 26 (1997) 1284 − 1309
31. Lothaire, M.: Combinatorics on Words. Encyclopedia of Math. and its Applications. Addison Wesley Publishing Company (1983)
32. McNaughton, R., Papert, S.: Counter-Free Automata. MIT Press, Cambridge, Mass. (1971)
33. Mateescu, A., Paun, Gh., Rozenberg, G., Salomaa, A.: Simple splicing systems. Discrete Applied Mathematics 84 (1998) 145 − 163
34. Paun, Gh.: On the splicing operation. Discrete Applied Mathematics 70 (1996) 57 − 79
35. Paun, Gh.: Regular extended H systems are computationally universal. Journal of Automata, Languages and Combinatorics. 1:1 (1996) 27 − 36
36. Paun, Gh., Salomaa, A.: DNA computing based on the splicing operation. Mathematica Japonica 43:3 (1996) 607 − 632
37. Paun, Gh., Rozenberg, G., Salomaa, A.: Computing by splicing. Theoretical Computer Science 168:2 (1996) 321 – 336
38. Paun, Gh., Rozenberg, G., Salomaa, A.: DNA computing, New Computing Paradigms. Springer-Verlag (1998)
39. Perrin, D.: Finite Automata. In: van Leeuwen, J. (ed.): Handbook of Theoretical Computer Science, Vol. B. Elsevier (1990) 1 − 57
40. Pixton, D.: Splicing in abstract families of languages. Theoretical Computer Science 234 (2000) 135 − 166
41. Pixton, D.: Linear and Circular Splicing Systems. In: Proc. of 1st Int. Symp. On Int. in Neural and Biological Systems (1996) 181 − 188
42. Pixton, D.: Regularity of splicing languages. Discrete Applied Mathematics 69 (1996) 101 − 124
43. Reis, C., Thierren, G.: Reflective star languages and codes. Information and Control 42 (1979) 1 − 9
44. Schützenberger, M.-P.: Sur certaines opÉrations de fermeture dans le langages rationnels. Symposia Mathematica 15 (1975) 245 − 253
45. Siromoney, R.: Distributed Circular Systems. In: Pre-Proc. of Grammar Systems 2000, Austria
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
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