TY - GEN
T1 - Protein structure-based method for identifying horizontal gene transfer
AU - Santosh, Venkat R.B.
AU - Griep, Mark A.
AU - Revesz, Peter Z.
PY - 2011
Y1 - 2011
N2 - 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.
AB - 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.
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U2 - 10.1145/1992896.1992898
DO - 10.1145/1992896.1992898
M3 - Conference contribution
AN - SCOPUS:79959815597
SN - 9781450306263
T3 - ACM International Conference Proceeding Series
SP - 9
EP - 16
BT - Proceedings of the 4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11
T2 - 4th International C* Conference on Computer Science and Software Engineering 2011, C3S2E'11
Y2 - 16 May 2011 through 18 May 2011
ER -