title: k-mer sparse matrix model for genetic sequence and its applications in sequence comparison.
abstract: Based on the k-mer model for genetic sequence, a k-mer sparse matrix representation is proposed to denote the types and sites of k-mers appearing in a genetic sequence, and there exists a one-to-one relationship between a genetic sequence and its associated k-mer sparse matrix. With the singular value decomposition of the k-mer sparse matrix, the k-mer singular value vector is constructed and utilized to numerically quantify the characteristics of a genetic sequence. We investigate and evaluate the optimum value k(⁎) chosen for our k-mer sparse matrix model for genetic sequence. To show the usefulness of our k-mer sparse matrix model method, it is applied to the comparison of genetic sequences, and the results obtained fully demonstrate that our proposed method is very powerful in analyzing and determining the relationships of genetic sequences.
authors.affiliation: School of Information Engineering, Suihua University, Suihua 152061, PR China. Electronic address: wenjia198021@126.com.
authors.forename: Jia
authors.initials: J
authors.lastname: Wen
authors.affiliation: School of Agriculture and Hydraulic Engineering, Suihua University, Suihua 152061, PR China.
authors.forename: YuYan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Mathematical Sciences, Tsinghua University, Beijing 100084, PR China. Electronic address: yau@uic.edu.
authors.forename: Stephen S T
authors.initials: SS
authors.lastname: Yau
mesh_terms: D001483:Base Sequence / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D008957:Models, Genetic; D017421:Sequence Analysis / Q000379:methods*
keywords: Optimum value; Phylogenetic analysis; Singular value decomposition; k-mer Model