Three models for gene assembly in ciliates: a comparison

Abstract

We survey in this paper the main differences among three variants of an intramolecular model for gene assembly: the general, the simple, and the elementary models. We present all of them in terms of sorting signed permutations and compare their behavior with respect to: (i) completeness, (ii) confluence (with the notion defined in three different setups), (iii) decidability, (iv) characterization of the sortable permutations in each model, (v) sequential complexity, and (vi) experimental validation.

Computational Nature of Gene Assembly in Ciliates

“…In the simple versions of ld, hi, and dlad the pointers involved in the recombination are at a minimal distance from each other. It turns out that the simple model is able to explain the successful assemblies of all currently known micronuclear gene sequences, see [11,75,63]. We discuss in this section the molecular and the mathematical formulation of the simple model and indicate some interesting properties of the model.…”

“…Consequently, once two or more micronuclear MDSs are combined into a larger composite MDS, they can no longer be moved along the sequence. We discuss in this section only the simple model and refer for details of the elementary model to [42,43,63,69].…”

“…We only give here the definitions for the stringbased operations, where the mathematical formulation is more concise. For the other formulations, including the relationships among these models, we refer to [46,63,8].…”

The Structure of Elementary Strategies for Gene Assembly in Ciliates

“…the folds involved in each of the operations are restricted to contain at most one MDS; that MDS could only be an micronuclear MDS in the case of the elementary operations, and it could also be a composite MDS in the case of the simple intramolecular operations. For a recent review on general, simple and elementary operations we refer to [10].…”

Successful Elementary Gene Assembly Strategies

“…In other words, a gene pattern can be assembled by simple operations if and only if an arbitrarily chosen simple assembly strategy for the gene pattern is successful. We refer to [21,22] for the survey on simple and elementary operations.…”