Abstract
The simple intramolecular model for gene assembly in ciliates is particularly interesting because it can predict the correct assembly of all available experimental data, although it is not universal. The simple model also has a confluence property that is not shared by the general model. A previous formalization of the simple model through sorting of signed permutations is unsatisfactory because it effectively ignores one operation of the model and thus, it cannot be used to answer questions about parallelism in the model, or about measures of complexity. We propose in this paper a string-based model in which a gene is represented through its sequence of pointers and markers and its assembly is represented as a string rewriting process. We prove that this string-based model is equivalent to the permutation-based model as far as gene assembly is concerned, while it tracks all operations of the model.
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References
Cavalcanti, A., Clarke, T.H., Landweber, L.: MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates. Nucleic Acids Research 33, 396–398 (2005)
Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: Computation in Living Cells: Gene Assembly in Ciliates. Springer, Heidelberg (2003)
Ehrenfeucht, A., Prescott, D.M., Rozenberg, G.: Computational aspects of gene (un)scrambling in ciliates. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation, pp. 216–256. Springer, New York (2001)
Harju, T., Li, C., Petre, I., Rozenberg, G.: Parallelism in gene assembly. Natural Computing (2006)
Harju, T., Li, C., Petre, I., Rozenberg, G.: Complexity Measures for Gene Assembly. In: Tuyls, K., Westra, R., Saeys, Y., Nowé, A. (eds.) KDECB 2006. LNCS (LNBI), vol. 4366. Springer, Heidelberg (2007)
Harju, T., Li, C., Petre, I., Rozenberg, G.: Modelling simple operations for gene assembly. In: Chen, J., Jonoska, N., Rozenberg, G. (eds.) Nanotechnology: Science and Computation, pp. 361–376. Springer, Heidelberg (2006)
Landweber, L.F., Kari, L.: The evolution of cellular computing: Nature’s solution to a computational problem. In: Proceedings of the 4th DIMACS Meeting on DNA-Based Computers, Philadelphia, PA, pp. 3–15 (1998)
Landweber, L.F., Kari, L.: Universal molecular computation in ciliates. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation. Springer, New York (2002)
Langille, M., Petre, I.: Simple gene assembly is deterministic. Fundamenta Informaticae 72, 1–12 (2006)
Prescott, D.M., Ehrenfeucht, A., Rozenberg, G.: Molecular operations for DNA processing in hypotrichous ciliates. Europ. J. Protistology 37, 241–260 (2001)
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Brijder, R., Langille, M., Petre, I. (2007). A String-Based Model for Simple Gene Assembly. In: Csuhaj-Varjú, E., Ésik, Z. (eds) Fundamentals of Computation Theory. FCT 2007. Lecture Notes in Computer Science, vol 4639. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74240-1_15
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DOI: https://doi.org/10.1007/978-3-540-74240-1_15
Publisher Name: Springer, Berlin, Heidelberg
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