From Micro to Macro: How the Overlap Graph Determines the Reduction Graph in Ciliates
The string pointer reduction system (SPRS) and the graph pointer reduction system (GPRS) are important formal models of gene assembly in ciliates. The reduction graph is a useful tool for the analysis of the SPRS, providing valuable information about the way that gene assembly is performed for a given gene. The GPRS is more abstract than the SPRS – not all information present in the SPRS is retained in the GPRS. As a consequence the reduction graph cannot be defined for the GPRS in general, but we show that it can be defined if we restrict ourselves to the so-called realistic overlap graphs (which correspond to genes occurring in nature). Defining the reduction graph within the GPRS allows one to carry over from the SPRS to the GPRS several results that rely on the reduction graph.
KeywordsGene Assembly Label Graph Reduction Graph Reality Edge Breakpoint Graph
Unable to display preview. Download preview PDF.
- 4.Brijder, R., Hoogeboom, H.J., Rozenberg, G.: How overlap determines the macronuclear genes in ciliates. LIACS Technical Report 2007-02, [arXiv:cs.LO/0702171] (2007)Google Scholar
- 7.Harju, T., Petre, I., Rozenberg, G.: Formal properties of gene assembly: Equivalence problem for overlap graphs. In: Jonoska, N., Păun, G., Rozenberg, G. (eds.) Aspects of Molecular Computing. LNCS, vol. 2950, pp. 202–212. Springer, Heidelberg (2003)Google Scholar