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The graphical representation of protein sequences based on the physicochemical properties and its applications

Authors

  • Ping-An He,

    Corresponding author
    1. Department of Mathematics, College of Science, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
    • Department of Mathematics, College of Science, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
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  • Yan-Ping Zhang,

    1. Department of Mathematics, College of Science, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
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  • Yu-Hua Yao,

    1. Institute of Biochemistry, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
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  • Yi-Fa Tang,

    1. State Key Laboratory of Scientific and Engineering Computing, ICMSEC, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
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  • Xu-Ying Nan

    1. Institute of Biochemistry, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
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Abstract

Based on the chaos game representation, a 2D graphical representation of protein sequences was introduced in which the 20 amino acids are rearranged in a cyclic order according to their physicochemical properties. The Euclidean distances between the corresponding amino acids from the 2-D graphical representations are computed to find matching (or conserved) fragments of amino acids between the two proteins. Again, the cumulative distance of the 2D-graphical representations is defined to compare the similarity of protein. And, the examination of the similarity among sequences of the ND5 proteins of nine species shows the utility of our approach. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

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