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CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism

文献类型： 外文期刊

作者： Ren, Zilin 1 ; Jiang, Lili 1 ; Di, Yaxin 1 ; Zhang, Dufei 1 ; Gong, Jianli 4 ; Gong, Jianting 5 ; Jiang, Qiwei 1 ; Fu, Zhiguo 2 ; Sun, Pingping 2 ; Zhou, Bo 1 ; Ni, Ming 5 ;

作者机构： 1.Chinese Acad Agr Sci, Changchun Vet Res Inst, State Key Lab Pathogen & Biosecur, Key Lab Jilin Prov Zoonosis Prevent & Control, Changchun 130122, Peoples R China

2.Northeast Normal Univ, Sch Informat Sci & Technol, 2555 Jingyue St, Changchun 130117, Jilin, Peoples R China

3.Northeast Agr Univ, Coll Vet Med, Harbin 150038, Peoples R China

4.Wuhan Technol & Business Univ, Sch Artificial Intelligence, Wuhan 340000, Peoples R China

5.Inst Hlth Serv & Transfus Med, Deartment Regenerat Med, Beijing 100850, Peoples R China

期刊名称：BIOINFORMATICS （ 影响因子：4.4； 五年影响因子：7.6 ）

ISSN： 1367-4803

年卷期： 2024 年 40 卷 7 期

页码：

收录情况： SCI

摘要： Motivation Due to the varying delivery methods of mRNA vaccines, codon optimization plays a critical role in vaccine design to improve the stability and expression of proteins in specific tissues. Considering the many-to-one relationship between synonymous codons and amino acids, the number of mRNA sequences encoding the same amino acid sequence could be enormous. Finding stable and highly expressed mRNA sequences from the vast sequence space using in silico methods can generally be viewed as a path-search problem or a machine translation problem. However, current deep learning-based methods inspired by machine translation may have some limitations, such as recurrent neural networks, which have a weak ability to capture the long-term dependencies of codon preferences.Results We develop a BERT-based architecture that uses the cross-attention mechanism for codon optimization. In CodonBERT, the codon sequence is randomly masked with each codon serving as a key and a value. In the meantime, the amino acid sequence is used as the query. CodonBERT was trained on high-expression transcripts from Human Protein Atlas mixed with different proportions of high codon adaptation index codon sequences. The result showed that CodonBERT can effectively capture the long-term dependencies between codons and amino acids, suggesting that it can be used as a customized training framework for specific optimization targets.Availability and implementation CodonBERT is freely available on https://github.com/FPPGroup/CodonBERT.

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