Gene assembly in Ciliates

Robustness of ciliates gene assembly

Ciliates are highly complex single-cell organisms, yet very successful from evolutionary point of view they emerged eon years ago and derived into many thousands of known species. Robustness may have an essential contribution to their survival. In this paper, we discuss the robustness of ciliates gene assembly, a process that transforms a diploid micronucleus to a macronucleus and involves mass...

Computational Nature of Gene Assembly in Ciliates

reduction graphs be ARG. It turns out that there are graphs in ARG that are not (isomorphic to) reduction graphs. To obtain a characterization we need one more property of reduction graphs: the ability to linearly order the vertices to resemble its (in general not unique) underlying legal string, as done in Fig. 11. To make this linear order of vertices explicit, we introduce a third set of edg...

The Algebra of Gene Assembly in Ciliates

The formal theory of intramolecular gene assembly in ciliates is fitted into the well-established theories of Euler circuits in 4-regular graphs, principal pivot transformations, and delta-matroids.

Two Models for Gene Assembly in Ciliates

Two models for gene assembly in ciliates have been proposed and investigated in the last few years. The DNA manipulations postulated in the two models are very different: one model is intramolecular – a single DNA molecule is involved here, folding on itself according to various patterns, while the other is intermolecular – two DNA molecules may be involved here, hybridizing with each other. Co...

Gene Assembly in Ciliates: Formal frameworks