Michal Burger. Atomization of DNA Sequences with Complex Evolutionary History. Master thesis, Comenius University in Bratislava, 2010. Supervised by Tomáš Vinař.
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DNA sequences which have undergone repeated duplications provide a significant challenge to DNA sequence analysis. Such sequences are believed to be a major source of evolutionary innovation, possibly being responsible for the rapid evolution of human species, and are of great interest to molecular biologists. Their analysis is difficult due to the many repeating regions which cause existing techniques to become unusable. Some of the new approaches to analyzing these sequences rely on finding the atomization of a set of related DNA sequences. Currently, there are no known algorithms that would produce atomizations of required quality and precision. This thesis proposes a new atomization algorithm and attempts to estimate its effectiveness. We have tested our approach both real and simulated data and, the results are compared to an existing atomization algorithm.