title: Whole-proteome based phylogenetic tree construction with inter-amino-acid distances and the conditional geometric distribution profiles.
abstract: There has been a growing interest in alignment-free methods for whole genome comparison and phylogenomic studies. In this study, we propose an alignment-free method for phylogenetic tree construction using whole-proteome sequences. Based on the inter-amino-acid distances, we first convert the whole-proteome sequences into inter-amino-acid distance vectors, which are called observed inter-amino-acid distance profiles. Then, we propose to use conditional geometric distribution profiles (the distributions of sequences where the amino acids are placed randomly and independently) as the reference distribution profiles. Last the relative deviation between the observed and reference distribution profiles is used to define a simple metric that reflects the phylogenetic relationships between whole-proteome sequences of different organisms. We name our method inter-amino-acid distances and conditional geometric distribution profiles (IAGDP). We evaluate our method on two data sets: the benchmark dataset including 29 genomes used in previous published papers, and another one including 67 mammal genomes. Our results demonstrate that the new method is useful and efficient.
authors.affiliation: Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan 411105, PR China; School of Mathematics and Computer Science, Gannan Normal University, Jiangxi 341000, PR China. Electronic address: xxianhua@sina.com.cn.
authors.forename: Xian-Hua
authors.initials: XH
authors.lastname: Xie
authors.affiliation: Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan 411105, PR China; School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: yuzuguo@aliyun.com.
authors.forename: Zu-Guo
authors.initials: ZG
authors.lastname: Yu
authors.affiliation: Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan 411105, PR China. Electronic address: korea10282003@163.com.
authors.forename: Guo-Sheng
authors.initials: GS
authors.lastname: Han
authors.affiliation: Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan 411105, PR China. Electronic address: yangweifeng09@163.com.
authors.forename: Wei-Feng
authors.initials: WF
authors.lastname: Yang
authors.affiliation: School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: v.anh@qut.edu.au.
authors.forename: Vo
authors.initials: V
authors.lastname: Anh
mesh_terms: D000596:Amino Acids / Q000032:analysis* / Q000737:chemistry; D000818:Animals; D001483:Base Sequence; D030541:Databases, Genetic; D016678:Genome / Q000235:genetics; D008322:Mammals / Q000235:genetics; D010802:Phylogeny; D020543:Proteome / Q000032:analysis* / Q000737:chemistry* / Q000235:genetics
chemical_list: D000596:Amino Acids; D020543:Proteome
keywords: Alignment-free whole-proteome comparison; Conditional geometric distribution profile; Inter-amino-acid distances; Phylogenetic tree