Formal Model and Simulation of the Gene Assembly Process in Ciliates
Date
2013-12-05
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
ORCID
Type
Degree Level
Masters
Abstract
The construction process of the functional macronucleus in certain types of ciliates is known as the
ciliate gene assembly process. It consists of a massive amount of DNA excision from the micronucleus and the rearrangement of the rest of the DNA sequences (in the case of stichotrichous ciliates). While several computational models have tried to represent certain parts of the gene assembly process, the real process remains not completely understood. In this research, a new formal model called the Computational 2JLP model is introduced based on the recent biological 2JLP model.
For justifying the formal model, a simulation is created and tested with real data. Several parameters are
introduced in the model that are used to test ambiguities or edge cases of the biological model. Parameters are systematically tested from the simulation to try to find their optimal values. Interestingly, a negative correlation is found between a parameter (which is used to filter out scnRNAs that are similar to IES specific sequences from the macronucleus) and the outcome of the simulation. It indicates that if a scnRNA consists of both an MDS and IES, then from the perspective of maximizing the outcome of the simulation, it is desirable to filter out this scnRNA.
The simulator successfully performs the gene assembly process whether the inputs are scrambled or
unscrambled DNA sequences. It is desirable for this model to serve as a foundation for future computational and mathematical study, and to help inform and refine the biological model.
Description
Keywords
Computational 2JLP model, gene assembly, ciliates
Citation
Degree
Master of Science (M.Sc.)
Department
Computer Science
Program
Computer Science