A1 Journal article (refereed)
SoftVoting6mA : An improved ensemble-based method for predicting DNA N6-methyladenine sites in cross-species genomes (2024)
Yin, Z., Lyu, J., Zhang, G., Huang, X., Ma, Q., & Jiang, J. (2024). SoftVoting6mA : An improved ensemble-based method for predicting DNA N6-methyladenine sites in cross-species genomes. Mathematical Biosciences and Engineering, 21(3), 3798-3815. https://doi.org/10.3934/mbe.2024169
JYU authors or editors
Publication details
All authors or editors: Yin, Zhaoting; Lyu, Jianyi; Zhang, Guiyang; Huang, Xiaohong; Ma, Qinghua; Jiang, Jinyun
Journal or series: Mathematical Biosciences and Engineering
ISSN: 1547-1063
eISSN: 1551-0018
Publication year: 2024
Publication date: 19/02/2024
Volume: 21
Issue number: 3
Pages range: 3798-3815
Publisher: American Institute of Mathematical Sciences
Publication country: United States
Publication language: English
DOI: https://doi.org/10.3934/mbe.2024169
Research data link: https://github.com/yinzhaoting/Softvoting-6mA
Publication open access: Openly available
Publication channel open access: Open Access channel
Abstract
The DNA N6-methyladenine (6mA) is an epigenetic modification, which plays a pivotal role in biological processes encompassing gene expression, DNA replication, repair, and recombination. Therefore, the precise identification of 6mA sites is fundamental for better understanding its function, but challenging. We proposed an improved ensemble-based method for predicting DNA N6-methyladenine sites in cross-species genomes called SoftVoting6mA. The SoftVoting6mA selected four (electron–ion-interaction pseudo potential, One-hot encoding, Kmer, and pseudo dinucleotide composition) codes from 15 types of encoding to represent DNA sequences by comparing their performances. Similarly, the SoftVoting6mA combined four learning algorithms using the soft voting strategy. The 5-fold cross-validation and the independent tests showed that SoftVoting6mA reached the state-of-the-art performance. To enhance accessibility, a user-friendly web server is provided at http://www.biolscience.cn/SoftVoting6mA/.
Keywords: DNA; gene expression; machine learning; neural networks (information technology); servers; bioinformatics
Free keywords: DNA N6-methyladenine; convolution neural network; soft voting; cross-species; feature fusion; webserver
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