Formal systems for gene assembly in ciliates
Theoretical Computer Science
String and graph reduction systems for gene assembly in ciliates
Mathematical Structures in Computer Science
Gene assembly in ciliates: computing by folding and recombination
A half-century of automata theory
How ciliates manipulate their own DNA – A splendid example of natural computing
Natural Computing: an international journal
DNA recombination through assembly graphs
Discrete Applied Mathematics
Computational processes in living cells: gene assembly in ciliates
DLT'02 Proceedings of the 6th international conference on Developments in language theory
Rewriting rule chains modeling DNA rearrangement pathways
Theoretical Computer Science
Four-regular graphs with rigid vertices associated to DNA recombination
Discrete Applied Mathematics
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We present in this paper a graph theoretical model of gene assembly, where (segments of) genes are distributed over a set of circular molecules. This model is motivated by the process of gene assembly in ciliates, but it is more general. In this model a set of circular DNA molecules is represented by a bicoloured and labelled graph consisting of cyclic graphs, and the recombination takes place in two stages: first, by folding *P with respect to a set P of pairs of vertices of the graph (representing pointers in the micronuclear genes of the ciliate), and secondly, by unfolding the so obtained graph to P with respect to vertices of higher valency. The final graph P is again a set of bicoloured cyclic graphs, where the genes are present as maximal monochromatic paths. Thus, the process of gene assembly corresponds to the dynamic process of changing cyclic graph decompositions. We show that the operation is well behaved in many respects, and that there is a sequence of pointer sets P1,...,Pm consisting of one or two pairs such that P=(((P1)P2)Pm) and each intermediate step I=(((P1)P2)Pi) is intracyclic, that is, the segments of a gene that lie in the same connected component of I, will lie in the same connected component of the successor graph I+1.