title: A measure of DNA sequence dissimilarity based on free energy of nearest-neighbor interaction.
abstract: We develop a novel method of asserting the similarity between two biological sequences without the need for alignment. The proposed method uses free energy of nearest-neighbor interactions as a simple measure of dissimilarity. It is used to perform a search for similarities of a query sequence against three complex datasets. The sensitivity and selectivity are computed and evaluated and the performance of the proposed distance measure is compared. Real data analysis shows that is a very efficient, sensitive and high-selective algorithm in comparing large dataset of DNA sequences.
authors.affiliation: Department of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China. zhangys@sdu.edu.cn
authors.forename: Yusen
authors.initials: Y
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D019277:Entropy; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D013816:Thermodynamics