Protein structure-based method for identifying horizontal gene transfer

Venkat R.B. Santosh, Mark A. Griep, Peter Z. Revesz

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

2 Citations (Scopus)

Abstract

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 paper 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 paper also considers visual structural comparisons and sequence alignments using the 'Jmol' tool. Finally, the paper considers the possibility that the methods yield false positives.

Original languageEnglish (US)
Title of host publicationProceedings of the 4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11
Pages9-16
Number of pages8
DOIs
StatePublished - Jul 6 2011
Event4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11 - Montreal, QC, Canada
Duration: May 16 2011May 18 2011

Publication series

NameACM International Conference Proceeding Series

Conference

Conference4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11
CountryCanada
CityMontreal, QC
Period5/16/115/18/11

Fingerprint

Gene transfer
Proteins
Bacteria
Genetic engineering
Genes

ASJC Scopus subject areas

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications

Cite this

Santosh, V. R. B., Griep, M. A., & Revesz, P. Z. (2011). Protein structure-based method for identifying horizontal gene transfer. In Proceedings of the 4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11 (pp. 9-16). (ACM International Conference Proceeding Series). https://doi.org/10.1145/1992896.1992898

Protein structure-based method for identifying horizontal gene transfer. / Santosh, Venkat R.B.; Griep, Mark A.; Revesz, Peter Z.

Proceedings of the 4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11. 2011. p. 9-16 (ACM International Conference Proceeding Series).

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

Santosh, VRB, Griep, MA & Revesz, PZ 2011, Protein structure-based method for identifying horizontal gene transfer. in Proceedings of the 4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11. ACM International Conference Proceeding Series, pp. 9-16, 4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11, Montreal, QC, Canada, 5/16/11. https://doi.org/10.1145/1992896.1992898
Santosh VRB, Griep MA, Revesz PZ. Protein structure-based method for identifying horizontal gene transfer. In Proceedings of the 4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11. 2011. p. 9-16. (ACM International Conference Proceeding Series). https://doi.org/10.1145/1992896.1992898
Santosh, Venkat R.B. ; Griep, Mark A. ; Revesz, Peter Z. / Protein structure-based method for identifying horizontal gene transfer. Proceedings of the 4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11. 2011. pp. 9-16 (ACM International Conference Proceeding Series).
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