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Abstract

Every organism has a genome. In some organisms, like mammals, genomes are highly repetitive. Repetitive genomic regions are associated with multiple biological functions as they can influence genome organization and gene regulation. Therefore, considerable importance is placed on identifying, localizing and categorizing them. Perhaps less studied but also important is the identification and categorization of unique genomic regions. Although unique regions have been associated with housekeeping and developmental genes and are thus crucial for survival, there is a distinct lack of bioinformatic tools for specifically finding unique regions in genomic sequences.


This thesis explores existing tools for finding unique genomic regions, expands their application domains, and establishes workflows for applying them in comparative genomics.

This thesis also contributes to the toolkit of comparative genomics by improving existing tools and integrating them into scaleable workflows for the detection of unique regions. Once detected, the unique regions are investigated for their functional content in mammals (Chapters 2 and 4), and for their suitability as diagnostic markers in bacteria (Chapter 3).