Soňa Gibaštíková. Finding Conserved Gene Clusters in Duplicated Genomes. Master thesis, Comenius University in Bratislava, 2014. Supervised by Broňa Brejová.

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The purpose of this thesis is finding conserved gene clusters in
genomes that have underwent the whole genome duplication. Gene
clusters are regions of genes conserved in several genomes that
have virtually the same function and their identifications have
many applications in genomics. In our thesis we formally define
the problem of finding gene clusters in duplicated genomes and
propose an algorithm based on dynamic programming solving the
problem in polynomial time. We develop several heuristic
improvements decreasing the computation time and we test our
model on biological and generated data.