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Graph theory is a branch of mathematics that has various applications in many different fields including computer science, physics, chemistry, pharmacy, biology and bioinformatics. A graph consists of a set of points (nodes) together with lines (edges) joining certain pairs of these nodes. These nodes and edges could be anything but in this study they are 3-dimensional coordinates of RNA (Ribo Nucleic Acid) tertiary structures. This thesis develops a framework for comparing RNA structures using graph theory, which has been named the CORONATION (Comparison Of RibO Nucleic Acid Tertiary's Involving Overlapping Networks).