Repetitive element array based genome analysis and application

Abstract

Since the first human genome was reported to be decoded by the human genome project in 2001, many researchers and scientists in chemistry and engineering as well as molecular biology have studied genomics. Up to now, almost researches on genomics haves focused on the gene study. Genes, however, are reported to constitute only 2~3% of the human genome, whereas repetitive elements (REs) make up a large portion of genomes of human and other eukaryotes. Current RE studies mainly deal with the known specific REs although many REs have not yet been analyzed and various REs are highly organized in genomes. Thus, in this thesis, we hypothesize that highly ordered RE arrays are associated with evolution and contribute many biological phenomena, and verify the hypothesis through the systematic analysis of the DNA sequence based on RE array. Furthermore, we present an application that uses the unique structure of RE and RE array. First, we develop a program to find RE arrays from the large size of genomes. Previous programs mainly detect the reported REs and deal with the small sized genomes. However, the RE search program in this thesis handles all unknown REs as well as the known REs. Also, chromosome-wide or species-wide genome analysis is necessary since REs exist in almost regions of a genome and individual RE has biologic effect to other REs. We make efficient algorithms and optimize the program structure to maximize the computational efficiency with low computing resources. We, also, develop a visualization program to see the RE array patterns and their characteristics. Second, we analyze the structure of multiple tandem repeat arrays of the human genome based on the systematic approach. The multiple tandem repeat arrays are very highly structured and organized in the human genome, so they are expected to have an important role in various biological phenomena. In addition, systematic analysis should be used to analyze the multiple tandem repeat arrays that are ver...