Gene Assembly in Ciliates Part II. Formal frameworks

Gene Assembly in Ciliates: Formal frameworks

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.

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...

Graph Polynomials Motivated by Gene Rearrangements in Ciliates

Gene rearrangements within the process of gene assembly in ciliates can be represented using a 4-regular graph. Based on this observation, Burns et al. [Discrete Appl. Math., 2013] propose a graph polynomial abstracting basic features of the assembly process, like the number of segments excised. We show that this assembly polynomial is essentially (i) a single variable case of the transition po...

Cryptanalysis of a Substitution-Permutation Network Using Gene Assembly in Ciliates

In this paper we provide a novel approach for breaking a significant class of block ciphers, the so-called SPN ciphers, using the process of gene assembly in ciliates. Our proposed scheme utilizes, for the first time, the Turing-powerful potential of gene assembly procedure of ciliated protozoa into the real world computations and has a fewer number of steps than the other proposed schemes to b...