RNA independent fragment partition method based on deep learning for RNA secondary structure prediction

The non-coding RNA secondary structure largely determines its function. Hence, accuracy in structure acquisition is of great importance. Currently, this acquisition primarily relies on various computational methods. The prediction of the structures of long RNA sequences with high precision and reasonable computational cost remains challenging. Here, we propose a deep learning model, RNA-par, which could partition an RNA sequence into several independent fragments (i-fragments) based on its exterior loops. Each i-fragment secondary structure predicted individually could be further assembled to acquire the complete RNA secondary structure. In the examination of our independent test set, the average length of the predicted i-fragments was 453 nt, which was considerably shorter than that of complete RNA sequences (848 nt). The accuracy of the assembled structures was higher than that of the structures predicted directly using the state-of-the-art RNA secondary structure prediction methods. This proposed model could serve as a preprocessing step for RNA secondary structure prediction for enhancing the predictive performance (especially for long RNA sequences) and reducing the computational cost. In the future, predicting the secondary structure of long-sequence RNA with high accuracy can be enabled by developing a framework combining RNA-par with various existing RNA secondary structure prediction algorithms. Our models, test codes and test data are provided at https://github.com/mianfei71/RNAPar.