AAAI Publications, Ninth Symposium of Abstraction, Reformulation, and Approximation

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Approximate Search on Protein Structures for Identification of Horizontal Gene Transfer in Bacteria
Swetha Billa, Mark Griep, Peter Revesz

Last modified: 2011-12-14

Abstract


Horizontal Gene Transfer (HGT) 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 paper presents an HGT identification method based on approximate searches on bacterial protein structures. This method makes use of Z- score similarities between the protein structures and also uses functions of BLAST and DaliLite to work with protein sequence and structural similarities. In addition, Jmol, a java viewer tool is used for visual structural comparisons and sequence alignment. We also present experimental results regarding HGTs between the Firmicutes bacterium Bacillus subtilis and various Proteobacteria bacteria.

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