Three‐unit semicircles curve: A compact 3D graphical representation of DNA sequences based on classifications of nucleotides |
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| Authors: | Yushuang Li Yufang Qin Xiaoqi Zheng Yu Zhang |
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| Institution: | 1. School of Science, Yanshan University, Qinhuangdao 066004, China;2. College of Information Technology, Shanghai Ocean University, Shanghai 201306, China;3. Department of Mathematics, Shanghai Normal University, Shanghai 200234, China;4. Scientific Computing Key Laboratory of Shanghai Universities, Shanghai 200234, ChinaFax: (+86) 21 64324284;5. Department of Computer, Shijiazhuang Post and Telecommunications Technical College, Shijiazhuang 050021, China |
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| Abstract: | A new three‐dimensional graphical representation of DNA sequences, three‐unit semicircles (TUS)‐curve, which maps a given sequence into a dot sequences embedded in three‐unit semicircles, is proposed based on three biclassifications of nucleotides. TUS‐curve has the merit of compactness and could avoid the degeneracy and loss of information. The geometrical center of the curve, which indicates the distribution of base frequencies of the corresponding DNA sequence, is extracted and applied to analyze the similarity of various species. Phylogenetic tree of 11 species based on their first exons of β‐globin genes showed that the TUS‐curve is a powerful tool to get valuable biological information. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011 |
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| Keywords: | graphical representation biclassification invariant similarity analysis phylogenetic tree |
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