Detection of Horizontal Gene Transfer in Bacterial Genomes

摘要：

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.

关键词： Horizontal gene transfer SVM Vector Quantization NPPC bacterial genome

作者: Hui Ning Bing Yang Jun Cui Ling Jing

作者单位: College of Science,China Agricultural University,Beijing 100083,P.R.China Xinjiang Radio & TV University,830049,Urumuqi,P.R.China

会议类型: 国际会议

会议名称: The 3rd International Symposium on Optimization and System Biology(第三届最优化与系统生物学国际会议 OSB09)

会议地点: 张家界

会议语种:英文

页码: 229-236

在线出版日期: 2009-09-20（万方平台首次上网日期，不代表论文的发表时间）