Protein Structure – Based Method for Identification of Horizontal Gene Transfer in Bacteria

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. iv Acknowledgements I am heartily thankful to my supervisor Dr. Peter Revesz for accepting me as his student and for providing me the opportunity to work with Bioinformatics. I would also like to thank him for his encouragement, guidance and unfailing support throughout the completion of this thesis. I owe my deepest gratitude to Prof. Mark Griep for taking time out of his busy schedule and providing his valuable expertise and guiding me through the completion of this thesis. I would also like to thank Prof. Jitender Deogun for agreeing to be on my committee and for providing valuable feedback and comments on my thesis. I am grateful for my dearest friend Venkat Ram Santosh for his motivation and encouragement in a number of ways. I would also like to thank Dipty Singh for always being there for me. I would like to thank my parents for always being supportive of me and believing that I could get through this, my brother and sister for giving me inspiration. Lastly, I offer my regards …