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This dissertation, "Analysis of DNA Shuffling by Computer Simulation" by Wing-hong, Hon, 韓永康, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author.
Abstract:
Abstract of thesis entitled \Analysis of DNA Shuing by Computer Simulation" Submitted by HON Wing Hong for the degree of Master of Philosophy at The University of Hong Kong in December 2003 Enzymes are widely used as chemical catalysts in industrial and commercial appli- cations. They are sometimes required to work under extreme conditions such as low pH or high temperature. However, enzymes found in nature cannot function properly under such conditions. Therefore, developing enzymes with improved performance that can work under dened and application-specic conditions is important. One common method is by DNA shuing. In DNA shuing, parameters such as initial fragment size, annealing temper- ature, and number of shuing rounds, can seriously in
uence the experimental results. Scientists want to nd out the optimal setting of these parameters in or- der to increase the probability of developing enzymes with the desired properties. However, this is not an easy task in practice. The large number of parameters requires us to test for many dierent settings, and thus we need to conduct many DNA shuing experiments. Furthermore, performing even a single experiment is very time consuming. Recently, several computational models for the DNA shuing experiment have been proposed. Scientists can now speed up the nding of the optimal setting by making use of the computer techniques. However, identication of the optimal settings is still time consuming because of the many parameters involved. It would therefore be helpful to identify some guidelines or observations that can reduce the search space. In this thesis, an improved computational model for the DNA shuing ex- periment is proposed, which is based on a model by Maheshri et al. Our model adheres closely to actual experimental conditions. Our simulation results show good agreement with the experimental results. In addition, studies were made on how homology, pattern of the match and mismatch positions of the parent genes, number of shuing rounds, initial frag- ment size and annealing temperature will aect the experimental results by usingthe proposed model and the computer generated data. Several observations have been drawn from these studies. These observations can help to reduce the search space for nding optimal settings in our simulation. If our observations are veri- ed by real experiments, they may provide useful information for scientists. The simulation program was written in C++ and run on a cluster (group of computers). The simulation program is
exible enough to be applied to a cluster of any size.
DOI: 10.5353/th_b2777102
Subjects:
DNA - Computer simulation
Gene fusion - Computer simulation
