Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation

• Published in: Journal of computational chemistry Vol. 29; no. 10; pp. 1632 - 1639
• Main Authors: Yao, Yu-hua, Dai, Qi, Nan, Xu-Ying, He, Ping-An, Nie, Zuo-Ming, Zhou, Song-Ping, Zhang, Yao-Zhou
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 30.07.2008; Wiley Subscription Services, Inc
• Subjects: Animals; Base Sequence; Chemistry; Computer Simulation; Correlation analysis; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; Eigenvalues; Euclidean space; Exons; Genes; Globins - genetics; graphical representation; Humans; Models, Chemical; Models, Genetic; Mutation; Nucleic Acid Conformation; Quantum Theory; Sensitivity analysis; similarity
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.20922

On the basis of a class of 2D graphical representations of DNA sequences, sensitivity analysis has been performed, showing the high-capability of the proposed representations to take into account small modifications of the DNA sequences. And sensitivity analysis also indicates that the absolute differences of the leading eigenvalues of the L/L matrices associated with DNA increase with the increase of the number of the base mutations. Besides, we conclude that the similarity analysis method based on the correlation angles can better eliminate the effects of the lengths of DNA sequences if compared with the method using the Euclidean distances. As application, the examination of similarities/dissimilarities among the coding sequences of the first exon of β-globin gene of different species has been performed by our method, and the reasonable results verify the validity of our method.