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FermatS: a novel numerical representation for protein sequence comparison and DNA-binding protein identification

Author(s):

Yanping Zhang*, Ya Gao, Jianwei Ni, Pengcheng Chen and Xiaosheng Wang   Pages 1 - 11 ( 11 )

Abstract:


Aim and Objective: Given the rapidly increasing number of molecular biology data available, computational methods of low complexity are necessary to infer protein structure, function, and evolution.

Method: In the work, we proposed a novel mthod, FermatS, which based on the global position information and local position representation from the curve and normalized moments of inertia, respectively, to extract features information of protein sequences. Furthermore, we use the generated features by FermatS method to analyze the similarity/dissimilarity of nine ND5 proteins and establish the prediction model of DNA-binding proteins based on logistic regression with 5-fold crossvalidation.

Results: In the similarity/dissimilarity analysis of nine ND5 proteins, the results are consistent with evolutionary theory. Moreover, this method can effectively predict the DNA-binding proteins in realistic situations.

Conclusion: The findings demonstrate that the proposed method is effective for comparing, recognizing and predicting protein sequences. The main code and datasets can download from https://github.com/GaoYa1122/FermatS..

Keywords:

Fermat spiral, Mass, Moment of inertia, Similarity/dissimilarity of species, Identification of DNA-binding proteins, Logistic regression.

Affiliation:

School of Mathematics and Physics Science and Engineering, Hebei University of Engineering, Handan 056038, PR, School of Mathematics and Physics Science and Engineering, Hebei University of Engineering, Handan 056038, PR, School of Mathematics and Physics Science and Engineering, Hebei University of Engineering, Handan 056038, PR, School of Mathematics and Physics Science and Engineering, Hebei University of Engineering, Handan 056038, PR, School of Mathematics and Physics Science and Engineering, Hebei University of Engineering, Handan 056038, PR



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