Summary
The gene assembly process that transforms the micronuclear genome to the macronuclear genome in stichotrichs ciliates is a complex DNA processing which is very interesting from the computational point of view. We shall give a survey of the notions and results concerning three molecular operations, known as ld, hi, and dlad, that have been postulated to accomplish the gene assembly process. These operations are modelled on three abstraction levels: MDS descriptors, legal strings, and overlap graphs. It turns out that these three abstractions are equivalent as far as the operational modelling of gene assembly is concerned.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D. M., Rozenberg, G., Formal systems for gene assembly in ciliates. Theor. Comput. Sci. 292, 199–219 (2003).
Ehrenfeucht, A., Harju, T., Petre, I., Rozenberg, G., Characterizing the micronuclear gene patterns in ciliates. Theory Comput. Syst. 35, 501–519 (2002).
Ehrenfeucht, A., Harju, T., Rozenberg, G., Gene assembly through cyclic graph decomposition. Theor. Comput. Syst. 281, 325–349 (2002).
Ehrenfeucht, A., Petre, I., Prescott, D. M., Rozenberg, G., Universal and simple operations for gene assembly in ciliates. In Words, Sequences, Languages: Where computer science, biology and linguistics come across, ed by Mitrana, V., Martin-Vide, C. (Kluwer Academic Publishers, Dortrecht/Boston 2001), 329–342.
Ehrenfeucht, A., Petre, I., Prescott, D. M., Rozenberg, G., String and graph reduction systems for gene assembly in ciliates. Math. Struct. Comput. Sci. 12, 113–134 (2001).
Ehrenfeucht, A., Petre, I., Prescott, D. M., Rozenberg, G., Circularity and other invariants of gene assembly in ciliates. In Words, semigroups, and transductions, ed by Ito, M., Păun, Gh., Yu, S. (World Scientific, Singapore 2001) pp 81–97.
Ehrenfeucht, A., Prescott, D. M., Rozenberg, G., Computational aspects of gene (un)scrambling in ciliates. In Evolution as Computation, ed by Landweber, L., Winfree, E. (Springer, Berlin Heidelberg New York 2001) pp 45–86.
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, ed by Kari, L., Rubin, H., Wood, D., Philadelphia, 1998, pp 3–15.
Landweber, L. F., Kari, L., Universal molecular computation in ciliates. In Evolution as Computation, ed by Landweber L., Winfree E. (Springer, Berlin Heidelberg New York 2002).
Păaun, Gh., Rozenberg, G., Salomaa, A., DNA Computing (Springer, Berlin Heidelberg New York 1998).
Prescott, D. M., Cutting, splicing, reordering, and elimination of DNA sequences in hypotrichous ciliates. BioEssays 14, 317–324 (1992).
Prescott, D. M., The unusual organization and processing of genomic DNA in hypotrichous ciliates. Trends Genet. 8, 439–445 (1992).
Prescott, D. M., The DNA of ciliated protozoa. Microbiol. Rev. 58(2), 233–267 (1994).
Prescott, D. M., The evolutionary scrambling and developmental unscabling of germlike genes in hypotrichous ciliates. Nucleic Acids Res. 27, 1243–1250 (1999).
Prescott, D. M., Genome gymnastics: unique modes of DNA evolution and processing in ciliates. Nat. Rev. Genet. 1(3), 191–198 (2000).
Prescott, D. M., DuBois, M., Internal eliminated segments (IESs) of Oxytrichidae. J. Eukariot. Microbiol. 43, 432–441 (1996).
Prescott, D. M., Ehrenfeucht, A., Rozenberg, G., Molecular operations for DNA processing in hypotrichous ciliates. Eur. J. Protistol. 37, 241–260 (2001).
Prescott, D. M., Rozenberg, G., How ciliates manipulate their own DNA — A splendid example of natural computing. Nat. Comput. 1, 165–183 (2002).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G. (2004). Modelling Gene Assembly in Ciliates. In: Ciobanu, G., Rozenberg, G. (eds) Modelling in Molecular Biology. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18734-6_5
Download citation
DOI: https://doi.org/10.1007/978-3-642-18734-6_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-62269-4
Online ISBN: 978-3-642-18734-6
eBook Packages: Springer Book Archive