Computer Science and Engineering, Department of


Date of this Version



A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Computer Science, Under the Supervision of Professor Peter Revesz and Professor Mark A. Griep. Lincoln, Nebraska: May, 2011
Copyright 2011 Swetha Billa


Horizontal Gene Transfer is defined as the movement of genetic material from one strain of species to another. Bacteria, being an asexual organism were always believed to transfer genes vertically. But recent studies provide evidence that shows bacteria can also transfer genes horizontally.

HGT plays a major role in evolution and medicine. It is the major contributor in bacterial evolution, enabling species to acquire genes to adapt to the new environments. Bacteria are also believed to develop drug resistance to antibiotics through the phenomenon of HGT. Therefore further study of HGT and its implications is necessary to understand the effects of HGT in biology and to study techniques to enable or disable the process based on its effects.

Methods to detect HGT events have been studied extensively but no method can accurately detect all the transfers between the organisms. This thesis discusses the various methods to detect HGT that were studied earlier and provides a new unique protein structure-based method to detect HGT in bacteria. This method makes use of Z-score similarities between the protein structures. This method uses functions of BLAST and DaliLite to work with protein sequence and structural similarities. Also ‘Jmol’, a java viewer tool is used for visual structural comparisons and sequence alignment. This thesis is an interdisciplinary effort, using both biological tools and computer algorithm to detect Horizontal Gene Transfer in bacteria.

Advisor: Peter Z. Revesz and Mark A. Griep