HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection
Joint Authors
Zheng, Huiwen
Yang, Yang
Xiao, Wanyue
Liu, Taigang
Sang, Xiuzhi
Source
Computational and Mathematical Methods in Medicine
Issue
Vol. 2020, Issue 2020 (31 Dec. 2020), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2020-03-28
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Prediction of DNA-binding proteins (DBPs) has become a popular research topic in protein science due to its crucial role in all aspects of biological activities.
Even though considerable efforts have been devoted to developing powerful computational methods to solve this problem, it is still a challenging task in the field of bioinformatics.
A hidden Markov model (HMM) profile has been proved to provide important clues for improving the prediction performance of DBPs.
In this paper, we propose a method, called HMMPred, which extracts the features of amino acid composition and auto- and cross-covariance transformation from the HMM profiles, to help train a machine learning model for identification of DBPs.
Then, a feature selection technique is performed based on the extreme gradient boosting (XGBoost) algorithm.
Finally, the selected optimal features are fed into a support vector machine (SVM) classifier to predict DBPs.
The experimental results tested on two benchmark datasets show that the proposed method is superior to most of the existing methods and could serve as an alternative tool to identify DBPs.
American Psychological Association (APA)
Sang, Xiuzhi& Xiao, Wanyue& Zheng, Huiwen& Yang, Yang& Liu, Taigang. 2020. HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection. Computational and Mathematical Methods in Medicine،Vol. 2020, no. 2020, pp.1-10.
https://search.emarefa.net/detail/BIM-1139324
Modern Language Association (MLA)
Sang, Xiuzhi…[et al.]. HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection. Computational and Mathematical Methods in Medicine No. 2020 (2020), pp.1-10.
https://search.emarefa.net/detail/BIM-1139324
American Medical Association (AMA)
Sang, Xiuzhi& Xiao, Wanyue& Zheng, Huiwen& Yang, Yang& Liu, Taigang. HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection. Computational and Mathematical Methods in Medicine. 2020. Vol. 2020, no. 2020, pp.1-10.
https://search.emarefa.net/detail/BIM-1139324
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1139324