title: An S-curve-based approach of identifying biological sequences.
abstract: The main idea of S-curve diagram is to assign different angle values (from 0 degrees to 180 degrees ) to different nucleotide acid residues or to different protein amino acids, and then according to cos alpha(j) and sin alpha(j), the values are accumulated to construct an S-curve diagram, which is in strict one-to-one correspondence with the biological sequence. In addition, the S-curve diagram proves to be without the degeneracy phenomenon, so that both the degeneracy problem represented by diagrams and the problem of visualization for biological sequence data are solved. Meanwhile, a new approach to differentiate the similarity of biological sequences--the degree of similarity--is put forward on the basis of the S-curve diagram. To put it in detail, the least square approach is first adopted to obtain a straight line equation according to the S-curve diagram, then according to the distance formula of the point to the straight line, the average ratio of square sum for the distance between the S-curve and the straight line is calculated, and finally, the similarity of the biological sequences is presented by the new standard--the degree of similarity. As is shown by the experimental results, the S-curve diagram can better represent biological sequences (such as protein's) within Cartesian coordinate system, and the mutation point of biological sequence. Thus, it turns out that the new standard-the degree of similarity is of obviously great advantage.
authors.affiliation: College of Computer, Northeast Normal University, 130117 Changchun, China. shzlp_1976@163.com
authors.forename: Lian-peng
authors.initials: LP
authors.lastname: Zhao
authors.forename: Ying-hua
authors.initials: YH
authors.lastname: Lv
authors.forename: Chun
authors.initials: C
authors.lastname: Li
authors.forename: Ming-hai
authors.initials: MH
authors.lastname: Yao
authors.forename: Xi-zi
authors.initials: XZ
authors.lastname: Jin
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D016678:Genome; D006657:Histones / Q000737:chemistry; D006801:Humans; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D006657:Histones; D011506:Proteins; D012313:RNA; D004247:DNA