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The Scientific World Journal
Volume 2012 (2012), Article ID 104269, 6 pages
http://dx.doi.org/10.1100/2012/104269
Research Article

Numerical Characterization of DNA Sequence Based on Dinucleotides

1School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China
2Department of Mathematics, West Virginia University, Morgantown, WV 26506, USA
3School of IOT Engineering, Jiangnan University, Wuxi 214122, China

Received 4 November 2011; Accepted 26 December 2011

Academic Editors: S. Cacchione and A. Pask

Copyright © 2012 Xingqin Qi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based on the frequencies of the dinucleotide XY in DNA sequences. The most important feature of this method is that it not only identifies adjacent XY pairs but also nonadjacent XY ones where X and Y are separated by some number of nucleotides. This methodology preserves information in DNA sequence that is ignored by other methods. We test our method on the coding regions of exon-1 of β–globin for 11 species, and the utility of this new method is demonstrated.