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.