Detection of Horizontal Gene Transfer in Bacterial Genomes

Most bacterial genes were acquired by horizontal gene transfer (HGT) from other prokaryotic organisms instead of being inherited by continuous vertical descent from an ancient ancestor. HGT is generally believed to be a major factor in microbiology evolution, allowing rapid diversification and adaptation. In this paper, we artificially simulate HGT by inserting phage genes into bacterial genomes, and then try to identify horizontally transferred genes from normal genes. Based on nucleotide composition analyses, Nonparallel Plane Proximal Classifier (NPPC) is applied to predict HGT for the first time. We also present a novel method, namely VQ-NPPC, which combines Vector Quantization (VQ) and NPPC. The results confirm that NPPC and VQ-NPPC show better performances than previous proposed methods i.e. C-Support Vector Classification(C-SVC) and One-class SVM for the detection of HGT.