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A novel graphical representation and similarity analysis of protein sequences based on physicochemical properties

Author

Listed:
  • Mahmoodi-Reihani, Mehri
  • Abbasitabar, Fatemeh
  • Zare-Shahabadi, Vahid

Abstract

One of popular topic in bioinformatics is protein sequence analysis. The graphical representation of protein sequence is a simple and common way to visualize protein sequences. In this study, a numerical descriptive vector for a given protein sequence is calculated based on twelve physicochemical properties of amino acids (AAs) and principal component analysis (PCA). Each entry of the descriptive vector corresponds to one AA in the sequence. By this vector, an intuitive spectrum-like graphical representation of protein sequence is proposed. Squared correlation coefficient as well as moving window correlation coefficient, as a new similarity/dissimilarity measure, were used to compare different sequences. Applicability of the proposed method is assessed by analyzing the nine ND5 proteins. The results revealed the utility of the proposed method.

Suggested Citation

  • Mahmoodi-Reihani, Mehri & Abbasitabar, Fatemeh & Zare-Shahabadi, Vahid, 2018. "A novel graphical representation and similarity analysis of protein sequences based on physicochemical properties," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 510(C), pages 477-485.
    • Handle: RePEc:eee:phsmap:v:510:y:2018:i:c:p:477-485
    DOI: 10.1016/j.physa.2018.07.011
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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.
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