Prediction of horizontal gene transfer in escherichia coil using machine learning

摘要

Horizontal Gene Transfer (HGT), also known as Lateral Gene Transfer is a process where an organism acquires genetic material from another organism without being a descendant of that organism. Horizontal gene transfer is said to be the predominant method of evolution in prokaryotic organisms. This study is focused on constructing a method that employs genome comparison and semi supervised learning to identify genes that are horizontally transferred to Escherichia coli 0157:H7 and attempting to find a link between these genes and other organisms that display pathogenic behaviour. E.coli 0157:H7 is compared to E.coli K-12 which is a harmless strain of the same organism. This comparison yields the set of genes that has not originated from the same ancestor (non-homologous) and is the possible cause of its pathogenic properties. A supervised self-organizing map was constructed to classify the non-homologous genes as either horizontally or vertically transferred. Most of the obtained horizontally transferred genes have shown a striking similarity to other pathological bacteria and Achaea. The results have indicated that, while it is possible to discern the mode of transfer of a gene based on compositional feature to a certain degree, it is better to combine several other features to further refine the findings.