Methods for Finding Structural Variations in DNA Barcodes

Abstract: Rapid spread of antibiotic resistance is currently one of the greatest threats to human health according to the World Health Organization [1] [2]. It is directly connected to horizontal gene transfer of plasmids, wherein resistance-coding genes often appear as structural variations (SVs). Therefore, developing comprehensive and rapid tools for detecting SVs is of great importance in both clinical biology and genomic research. Currently, many of the established DNA sequencing techniques require hours or even days [3] [4] to run and are consequently, in some instances, unfit for clinical settings. This thesis presents and compares three approaches for rapid identification of SVs based on optical DNA mapping, two of which are new to this thesis. Although not yet adequate for application in their current state, we justify the usage of some of the techniques in the novel algorithms. We also demonstrate how one of the techniques shows some promise and is open for future amends.