Computer Science and Engineering, Department of


Date of this Version

Spring 2-17-2011

Document Type



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: January, 2011
Copyright 2011 Venkat Ram B. Santosh.


Genetics has traditionally focused on vertical gene transfer, which is the passing of the genetic material of an organism to its offspring. However, recent studies in genetics increased the awareness that horizontal gene transfer, which is the passing of the genetic material of an organism to another organism that is not its offspring, is also a significant phenomenon. Horizontal gene transfer is thought to play a major role in the natural evolution of bacteria, such as, when several different types of bacteria all suddenly develop the same drug resistance genes. Artificial horizontal gene transfer occurs in genetic engineering.

This thesis provides methods to detect horizontal gene transfer among bacteria using BLAST and DaliLite measures of protein sequence and structural similarities. This research is novel and unique because no previous horizontal gene transfer study worked directly on protein sequences and structures. The main method is a computer algorithm to detect horizontal gene transfer among different COG classifications of proteins. The thesis also considers visual structural comparisons and sequence alignments using the ‘Jmol’ tool. Finally, the thesis considers the possibility that the method yields false positives.