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A new graphical representation of protein sequences and its applications

Author

Listed:
  • Hou, Wenbing
  • Pan, Qiuhui
  • He, Mingfeng

Abstract

Sequence analysis is one of the foundations in bioinformatics for the abundant information hidden in the sequences. It is helpful for scientists’ study on the function of DNA, proteins and cells. In this paper, we outline a novel method for protein sequences similarity analysis based on the physical–chemical properties of amino acids. We consider the protein sequence as a rigid-body with mass. Then we introduce the moment of inertia to the calculation of similarity of sequences and the sequences are transformed into vectors by the tensor for moment of inertia. The Euclidean distance is employed as a measurement of the similarities. At last, the comparison with other references’ results shows our approach is reasonable and effective.

Suggested Citation

  • 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.
    • Handle: RePEc:eee:phsmap:v:444:y:2016:i:c:p:996-1002
    DOI: 10.1016/j.physa.2015.10.067
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    References listed on IDEAS

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    1. 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.
    2. 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.
    3. 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.
    Full references (including those not matched with items on IDEAS)

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