Paper Info
Title
A classification model for lncRNA and mRNA based on k-mers and a convolutional neural network.
Abstract
Long-chain non-coding RNA (lncRNA) is closely related to many biological activities. Since its sequence structure is similar to that of messenger RNA (mRNA), it is difficult to distinguish between the two based only on sequence biometrics. Therefore, it is particularly important to construct a model that can effectively identify lncRNA and mRNA. First, the difference in the k-mer frequency distribution between lncRNA and mRNA sequences is considered in this paper, and they are transformed into the k-mer frequency matrix. Moreover, k-mers with more species are screened by relative entropy. The classification model of the lncRNA and mRNA sequences is then proposed by inputting the k-mer frequency matrix and training the convolutional neural network. Finally, the optimal k-mer combination of the classification model is determined and compared with other machine learning methods in humans, mice and chickens. The results indicate that the proposed model has the highest classification accuracy. Furthermore, the recognition ability of this model is verified to a single sequence. We established a classification model for lncRNA and mRNA based on k-mers and the convolutional neural network. The classification accuracy of the model with 1-mers, 2-mers and 3-mers was the highest, with an accuracy of 0.9872 in humans, 0.8797 in mice and 0.9963 in chickens, which is better than those of the random forest, logistic regression, decision tree and support vector machine.
Year
DOI
Venue
2019
10.1186/s12859-019-3039-3
BMC Bioinformatics
Keywords
DocType
Volume
lncRNA, mRNA, K-mers, Relative entropy, Convolutional neural network
Journal
20
Issue
ISSN
Citations 
1
1471-2105
1
PageRank 
References 
Authors
0.36
0
6
Name
Order
Citations
PageRank
Jianghui Wen110.36
Yeshu Liu210.36
Shi Yu3199.01
Haoran Huang410.36
Bing Deng5446.55
Xinping Xiao651.47