Abstract
The gene assembly process in ciliates (single-cell organisms) is interesting from both the biological and computational point of view. This paper studies the computational nature of the gene assembly process. Motivated by the breakpoint graph known from another branch of DNA transformation research, we introduce the reduction graph as a tool for the study of this process, and illustrate its usefulness by proving a number of properties of gene assembly.
This research was supported by the Netherlands Organization for Scientific Research (NWO) project 635.100.006 “VIEWS”.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Bergeron, A., Mixtacki, J., Stoye, J.: On sorting by translocations. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 615–629. Springer, Heidelberg (2005)
Cavalcanti, A.R.O.: Ciliates IES MDS Database, website: http://oxytricha.princeton.edu/dimorphism/
Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: String and graph reduction systems for gene assembly in ciliates. Mathematical Structures in Computer Science 12, 113–134 (2002)
Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: Computation in Living Cells: Gene Assembly in Ciliates. Springer, Heidelberg (2004)
Ehrenfeucht, A., Harju, T., Petre, I., Rozenberg, G.: Characterizing the micronuclear gene patterns in ciliates. Theory of Computing Systems 35, 501–519 (2002)
Meidanis, J., Setubal, J.C.: Introduction to Computational Molecular Biology. PWS Publishing Company (1997)
Pevzner, P.A.: Computational Molecular Biology: An Algorithmic Approach. MIT Press, Cambridge (2000)
Prescott, D.M., DuBois, M.: Internal eliminated segments (IESs) of Oxytrichidae. Journal of Eukariotic Microbiology 43, 432–441 (1996)
Prescott, D.M., Ehrenfeucht, A., Rozenberg, G.: Molecular operations for DNA processing in hypotrichous ciliates. European Journal of Protistology 37, 241–260 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Brijder, R., Hoogeboom, H.J., Rozenberg, G. (2005). The Breakpoint Graph in Ciliates. In: R. Berthold, M., Glen, R.C., Diederichs, K., Kohlbacher, O., Fischer, I. (eds) Computational Life Sciences. CompLife 2005. Lecture Notes in Computer Science(), vol 3695. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11560500_12
Download citation
DOI: https://doi.org/10.1007/11560500_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29104-6
Online ISBN: 978-3-540-31726-5
eBook Packages: Computer ScienceComputer Science (R0)