| Autor: |
Xingyu Tang, Peijie Zheng, Yuewu Liu, Yuhua Yao, Guohua Huang |
| Jazyk: |
angličtina |
| Rok vydání: |
2023 |
| Předmět: |
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| Zdroj: |
Mathematical Biosciences and Engineering, Vol 20, Iss 1, Pp 1037-1057 (2023) |
| Druh dokumentu: |
article |
| ISSN: |
1551-0018 |
| DOI: |
10.3934/mbe.2023048?viewType=HTML |
| Popis: |
DNase I hypersensitive sites (DHSs) are a specific genomic region, which is critical to detect or understand cis-regulatory elements. Although there are many methods developed to detect DHSs, there is a big gap in practice. We presented a deep learning-based language model for predicting DHSs, named LangMoDHS. The LangMoDHS mainly comprised the convolutional neural network (CNN), the bi-directional long short-term memory (Bi-LSTM) and the feed-forward attention. The CNN and the Bi-LSTM were stacked in a parallel manner, which was helpful to accumulate multiple-view representations from primary DNA sequences. We conducted 5-fold cross-validations and independent tests over 14 tissues and 4 developmental stages. The empirical experiments showed that the LangMoDHS is competitive with or slightly better than the iDHS-Deep, which is the latest method for predicting DHSs. The empirical experiments also implied substantial contribution of the CNN, Bi-LSTM, and attention to DHSs prediction. We implemented the LangMoDHS as a user-friendly web server which is accessible at http:/www.biolscience.cn/LangMoDHS/. We used indices related to information entropy to explore the sequence motif of DHSs. The analysis provided a certain insight into the DHSs. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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