Characterizing Reduction Graphs for Gene Assembly in Ciliates
The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the notion of breakpoint graph in the theory of sorting by reversal, for legal strings provide valuable insights into the gene assembly process. We characterize which legal strings obtain the same reduction graph (up to isomorphism), and moreover we characterize which graphs are (isomorphic to) reduction graphs.
Unable to display preview. Download preview PDF.
- 5.Bergeron, A., Mixtacki, J., Stoye, J.: On sorting by translocations. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P., Waterman, M. (eds.) Research in Computational Molecular Biology. LNCS (LNBI), vol. 3500, pp. 615–629. Springer, Heidelberg (2005)Google Scholar
- 6.Setubal, J., Meidanis, J.: Introduction to Computional Molecular Biology. PWS Publishing Company, London (1997)Google Scholar
- 7.Brijder, R., Hoogeboom, H., Muskulus, M.: Strategies of loop recombination in ciliates. LIACS Technical Report 2006-01, [arXiv:cs.LO/0601135] (2006)Google Scholar
- 9.Brijder, R., Hoogeboom, H.: The fibers and range of reduction graphs in ciliates. LIACS Technical Report 2007-01, [arXiv:cs.LO/0702041] (2007)Google Scholar