5 research outputs found
Reducibility of Gene Patterns in Ciliates using the Breakpoint Graph
Gene assembly in ciliates is one of the most involved DNA processings going
on in any organism. This process transforms one nucleus (the micronucleus) into
another functionally different nucleus (the macronucleus). We continue the
development of the theoretical models of gene assembly, and in particular we
demonstrate the use of the concept of the breakpoint graph, known from another
branch of DNA transformation research. More specifically: (1) we characterize
the intermediate gene patterns that can occur during the transformation of a
given micronuclear gene pattern to its macronuclear form; (2) we determine the
number of applications of the loop recombination operation (the most basic of
the three molecular operations that accomplish gene assembly) needed in this
transformation; (3) we generalize previous results (and give elegant
alternatives for some proofs) concerning characterizations of the micronuclear
gene patterns that can be assembled using a specific subset of the three
molecular operations.Comment: 30 pages, 13 figure
Models of natural computation : gene assembly and membrane systems
This thesis is concerned with two research areas in natural computing: the computational nature of gene assembly and membrane computing. Gene assembly is a process occurring in unicellular organisms called ciliates. During this process genes are transformed through cut-and-paste operations. We study this process from a theoretical point of view. More specifically, we relate the theory of gene assembly to sorting by reversal, which is another well-known theory of DNA transformation. In this way we obtain a novel graph-theoretical representation that provides new insights into the nature of gene assembly. Membrane computing is a computational model inspired by the functioning of membranes in cells. Membrane systems compute in a parallel fashion by moving objects, through membranes, between compartments. We study the computational power of various classes of membrane systems, and also relate them to other well-known models of computation.Netherlands Organisation for Scientific Research (NWO), Institute for Programming research and Algorithmics (IPA)UBL - phd migration 201
Sorting Permutations: Games, Genomes, and Cycles
Permutation sorting, one of the fundamental steps in pre-processing data for
the efficient application of other algorithms, has a long history in
mathematical research literature and has numerous applications. Two
special-purpose sorting operations are considered in this paper: context
directed swap, abbreviated cds, and context directed reversal, abbreviated cdr.
These are special cases of sorting operations that were studied in prior work
on permutation sorting. Moreover, cds and cdr have been postulated to model
molecular sorting events that occur in the genome maintenance program of
certain species of single-celled organisms called ciliates.
This paper investigates mathematical aspects of these two sorting operations.
The main result of this paper is a generalization of previously discovered
characterizations of cds-sortability of a permutation. The combinatorial
structure underlying this generalization suggests natural combinatorial
two-player games. These games are the main mathematical innovation of this
paper.Comment: to appear in Discrete Mathematics, Algorithms and Application