MRM-BERT

The code is the implementation of our method described in the paper “Ying Zhang, Fang Ge, Fuyi Li, Xibei Yang, Jiangning Song, and Dong-Jun Yu, Prediction of Multiple Types of RNA Modifications via Biological Language Model”.

(1) Environment setup:

Refer to https://github.com/jerryji1993/DNABERT#readme.

(2) Download the well-trained models of our method:

https://drive.google.com/drive/folders/13AG0ByRp_WKj8vg8r0Xj94vFjaoeGIJR

(3) For multi-sequence prediction:

code/main_Multi_prediction.py

(4) For single-sequence prediction and analysis

code/main_Single_att_analyse.py

(5) Fine-tune with pre-trained model

Refer to DNABERT, and pay attention to preprocessing the sequences into k-mer format.

(6) Contact

If you are interested in our work or have any suggestions or questions about our research work, please feel free to contact us. E-mail: yingzhang@njust.edu.cn.