The Algebra of Gene Assembly in Ciliates

Recombination faults in gene assembly in ciliates modeled using multimatroids

We formally model the process of gene assembly in ciliates on the level of individual genes using the notion of multimatroids introduced by Bouchet. Gene assembly involves heavy splicing and recombination, and it turns out that multimatroids form a suitable abstract model that captures essential features of this process. We use this abstract model to study the effect of faulty recombinations du...

Universal and simple operations for gene assembly in ciliates

The way that ciliates transform genes from their micronuclear to the macronuclear form is very interesting (and unique), also from a computational point of view. In this paper, we describe the model of gene assembly in ciliates presented in [2], [3], and [4]. Moreover, we prove that the set of three operations underlying this model is universal, in the sense that it suffices for gene assembly f...

Circularity and Other Invariants of Gene Assembly in Ciliates

Ciliates (an ancient group of single cell organisms) have two sorts of nuclei with different functionalities: the micronucleus and the macronucleus. After the cell mating the micronuclear genes are converted into the macronuclear genes in the process called gene assembly. This is one of the most complex examples of DNA processing known in any organisms, and it is fascinating from the computatio...

On computational properties of gene assembly in ciliates

Gene assembly in stichotrichous ciliates happening during sexual reproduction is one of the most involved DNA manipulation processes occurring in biology. This biological process is of high interest from the computational and mathematical points of view due to its close analogy with such concepts and notions in theoretical computer science as permutation and linked list sorting and string rewri...

Gene Assembly in Ciliates: Formal frameworks