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

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 diff...

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Bibliographic Details
Published in:Journal of computational chemistry 2008-07, Vol.29 (10), p.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: Article
Language:English
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
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Summary: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.
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.20922