Identification of DNA-Binding Proteins by Multiple Kernel Support Vector Machine and Sequence Information

Author(s): Yijie Ding, Feng Chen, Xiaoyi Guo*, Jijun Tang, Hongjie Wu*

Journal Name: Current Proteomics

Volume 17 , Issue 4 , 2020


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Abstract:

Background: The DNA-binding proteins is an important process in multiple biomolecular functions. However, the tradition experimental methods for DNA-binding proteins identification are still time consuming and extremely expensive.

Objective: In past several years, various computational methods have been developed to detect DNAbinding proteins. However, most of them do not integrate multiple information.

Methods: In this study, we propose a novel computational method to predict DNA-binding proteins by two steps Multiple Kernel Support Vector Machine (MK-SVM) and sequence information. Firstly, we extract several feature and construct multiple kernels. Then, multiple kernels are linear combined by Multiple Kernel Learning (MKL). At last, a final SVM model, constructed by combined kernel, is built to predict DNA-binding proteins.

Results: The proposed method is tested on two benchmark data sets. Compared with other existing method, our approach is comparable, even better than other methods on some data sets.

Conclusion: We can conclude that MK-SVM is more suitable than common SVM, as the classifier for DNA-binding proteins identification.

Keywords: DNA-binding proteins, feature extraction, support vector machine, multiple kernel learning, kernel alignment, binding sites.

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Article Details

VOLUME: 17
ISSUE: 4
Year: 2020
Published on: 28 June, 2020
Page: [302 - 310]
Pages: 9
DOI: 10.2174/1570164616666190417100509
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