Approximate search on protein structures for identification of Horizontal gene rransfer in bacteria

Swetha Billa, Mark A. Griep, Peter Z. Revesz

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

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 Zscore 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.

Original languageEnglish (US)
Title of host publicationSARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation
Pages18-25
Number of pages8
StatePublished - Dec 1 2011
Event9th Symposium on Abstraction, Reformulation, and Approximation, SARA 2011 - Cardona, Catalonia, Spain
Duration: Jul 17 2011Jul 18 2011

Publication series

NameSARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation

Conference

Conference9th Symposium on Abstraction, Reformulation, and Approximation, SARA 2011
CountrySpain
CityCardona, Catalonia
Period7/17/117/18/11

Fingerprint

Gene transfer
Bacteria
Genes
Proteins
Antibiotics
Bacilli
Medicine

ASJC Scopus subject areas

  • Computer Science Applications

Cite this

Billa, S., Griep, M. A., & Revesz, P. Z. (2011). Approximate search on protein structures for identification of Horizontal gene rransfer in bacteria. In SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation (pp. 18-25). (SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation).

Approximate search on protein structures for identification of Horizontal gene rransfer in bacteria. / Billa, Swetha; Griep, Mark A.; Revesz, Peter Z.

SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation. 2011. p. 18-25 (SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Billa, S, Griep, MA & Revesz, PZ 2011, Approximate search on protein structures for identification of Horizontal gene rransfer in bacteria. in SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation. SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation, pp. 18-25, 9th Symposium on Abstraction, Reformulation, and Approximation, SARA 2011, Cardona, Catalonia, Spain, 7/17/11.
Billa S, Griep MA, Revesz PZ. Approximate search on protein structures for identification of Horizontal gene rransfer in bacteria. In SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation. 2011. p. 18-25. (SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation).
Billa, Swetha ; Griep, Mark A. ; Revesz, Peter Z. / Approximate search on protein structures for identification of Horizontal gene rransfer in bacteria. SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation. 2011. pp. 18-25 (SARA 2011 - Proceedings of the 9th Symposium on Abstraction, Reformulation, and Approximation).
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