MCAMEF-BERT: an efficient deep learning method for RNA N7-methylguanosine site prediction via multi-branch feature integration

Accurate identification of N7-methylguanosine (m7G) modification sites plays a critical role in uncovering the regulatory mechanisms of various biological processes, including human development, tumor initiation, and progression. However, existing prediction methods still suffer from limited representational power, redundant feature fusion, insufficient utilization of biological prior knowledge, and poor interpretability. In this study, we propose a novel deep learning model named MCAMEF-BERT. This model adopts a parallel architecture that integrates both a DNABERT-2-based pretrained model branch and multiple traditional feature encoding branches, enabling comprehensive multi-perspective sequence feature extraction. To address the redundancy issue in feature fusion, we introduce a multi-channel attention module. Our model demonstrates superior accuracy and effectiveness on datasets from m7GHub, outperforming other state-of-the-art classifiers. Furthermore, we validate the interpretability of MCAMEF-BERT through in silico saturation mutagenesis experiments, and confirm its robustness in motif recognition. Moreover, its generalization capability is validated across diverse RNA modification site prediction tasks.