Dependency relations between elementary intramolecular operations in gene assembly in ciliates

A1 Journal article (refereed)


Internal Authors/Editors


Publication Details

List of Authors: Petre Ion, Rogojin Vladimir
Publisher: Otto-von-Guericke-Universitat, Magdeburg
Publication year: 2014
Journal: Journal of Automata, Languages and Combinatorics
Volume number: 19
Issue number: 1-4
Start page: 265
End page: 277


Abstract

The intramolecular model of gene assembly in ciliates postulates three foldingrecombination operations over a single DNA molecule. Those operations are suggested to assemble a macronuclear contiguous gene from its shuffled and inverted micronuclear fragments. The elementary intramolecular model considers DNA rearrangements containing at most one micronuclear gene fragment. In contrast with the general model, the elementary intramolecular operations are not universal: they cannot assemble all hypothetical micronuclear gene patterns. We investigate the following general question: what micronuclear gene patterns can be assembled by elementary intramolecular operations? Currently a number of efficient solutions exists for micronuclear gene patterns without inverted gene fragments. Going towards an efficient solution for the general question, we investigate in this paper the order relation between elementary intramolecular operations within assembly strategies applicable to gene patterns with inverted fragments.


Keywords

dependency graphs, elementary operations, gene assembly in ciliates, intramolecular operations, Signed permutations, Sorting

Last updated on 2019-25-06 at 06:28