Jaroslav Budiš. Discovering motifs in mitochondrial DNA. Master thesis, Comenius University in Bratislava, 2011. Supervised by Broňa Brejová.

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Motif discovery problem abstracts the task of discovering
conserved cluster of similar, relatively short substrings
in set of biological sequences. We analyse in depth motif
discovery algorithm MEME which we have also reimplemented.
We propose a new method for initializing the iterative
EM algorithm which is a core algorithm of the MEME.
In our tests it decreases the number of required iterations
compared to a the approach that is used in MEME.
We also propose additional changes to deal with specific
structure of mitochondrial genomes. In particular,
we adjusted MEME model to account for the existence
of GC islands, which are relatively short areas
significantly enriched in cytosine and guanine.
Discovery of patterns in these regions may eventually
lead to their classification and therefore provide
evidence of their conservation.