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A graphical representation of protein based on a novel iterated function system

Author

Listed:
  • Ma, Tingting
  • Liu, Yuxin
  • Dai, Qi
  • Yao, Yuhua
  • He, Ping-an

Abstract

In this article, a novel family of iterated function system (IFS) was introduced to outline a 2D graphical representation of protein sequences, which incorporates with various physicochemical properties of amino acids. Then a mathematical description was suggested to quantificationally compare the similarities and dissimilarities of protein sequences from their 2D curves. Based on this method, similarities/dissimilarities were compared among sequences of the ND5 proteins of nine different species, as well as sequences of eight ND6 proteins. The phylogenetic tree of the nine ND5 proteins was constructed according to Fuzzy cluster analysis. By correlation analysis, the ClustalW results were compared with our similarity/dissimilarity results and other graphical representation results to demonstrate the effectiveness of our approach.

Suggested Citation

  • Ma, Tingting & Liu, Yuxin & Dai, Qi & Yao, Yuhua & He, Ping-an, 2014. "A graphical representation of protein based on a novel iterated function system," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 403(C), pages 21-28.
    • Handle: RePEc:eee:phsmap:v:403:y:2014:i:c:p:21-28
    DOI: 10.1016/j.physa.2014.01.067
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    References listed on IDEAS

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    1. Li, Chun & Yu, Xiaoqing & Yang, Liu & Zheng, Xiaoqi & Wang, Zhifu, 2009. "3-D maps and coupling numbers for protein sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(9), pages 1967-1972.
    2. Abo el Maaty, Moheb I. & Abo-Elkhier, Mervat M. & Abd Elwahaab, Marwa A., 2010. "3D graphical representation of protein sequences and their statistical characterization," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(21), pages 4668-4676.
    3. He, Ping-an & Wei, Jinzhou & Yao, Yuhua & Tie, Zhixin, 2012. "A novel graphical representation of proteins and its application," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(1), pages 93-99.
    4. Yu, Hong-Jie & Huang, De-Shuang, 2012. "Novel graphical representation of genome sequence and its applications in similarity analysis," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(23), pages 6128-6136.
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    Cited by:

    1. Hou, Wenbing & Pan, Qiuhui & He, Mingfeng, 2016. "A new graphical representation of protein sequences and its applications," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 444(C), pages 996-1002.

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