title: Protein sequence analysis by incorporating modified chaos game and physicochemical properties into Chou's general pseudo amino acid composition.
abstract: In this contribution we introduced a novel graphical method to compare protein sequences. By mapping a protein sequence into 3D space based on codons and physicochemical properties of 20 amino acids, we are able to get a unique P-vector from the 3D curve. This approach is consistent with wobble theory of amino acids. We compute the distance between sequences by their P-vectors to measure similarities/dissimilarities among protein sequences. Finally, we use our method to analyze four datasets and get better results compared with previous approaches.
authors.affiliation: School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China.
authors.forename: Chunrui
authors.initials: C
authors.lastname: Xu
authors.affiliation: School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China.
authors.forename: Dandan
authors.initials: D
authors.lastname: Sun
authors.affiliation: School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China.
authors.forename: Shenghui
authors.initials: S
authors.lastname: Liu
authors.affiliation: School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China. Electronic address: zhangys@sdu.edu.cn.
authors.forename: Yusen
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D055598:Chemical Phenomena; D003062:Codon / Q000235:genetics; D005716:Game Theory; D006801:Humans; D017711:Nonlinear Dynamics; D010802:Phylogeny; D020539:Sequence Analysis, Protein / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism; D055544:beta-Globins
chemical_list: D000596:Amino Acids; D003062:Codon; D014157:Transcription Factors; D055544:beta-Globins
keywords: Codon; Hydropathy index; Isoelectric point; Protein vector; Sequences analysis