SpliceCannon: A novel framework for the prediction of canonical and non-canonical splice sites based on deep learning

Accurately predicting splice sites in DNA sequences is not only of utmost importance in the study of gene expression and protein synthesis, but also crucial to precisely understanding the pathogenesis of various diseases related to splicing. In the past few decades, several tools for identifying splice sites have been developed, however, many of them ignore the contextual influence in DNA sequences in the process of encoding, consequently leading to considerable false positives in prediction. Additionally, most methods solely investigate canonical splicing whereas pay little attention to non-canonical ones. To address the issues mentioned above, we propose a comprehensive method, SpliceCannon, for accurately predicting both canonical and non-canonical splice sites based on neural networks. This method uses the combination of k-nucleotide frequencies and Doc2vec to encode the sequence, then employs a series of comprehensive neural networks such as bidirectional long short-term memory networks and residual networks to effectively extract features from the original sequence while avoiding the problems such as gradient vanishing. The results demonstrate that our method consistently achieves high accuracy when tested on multiple species. Compared to other recent methods, our model exhibits superior performance, stronger generalization ability, and wider applicability. In particular, The recognition accuracy is also remarkably high on the non-canonical dataset. We envision that this proposed method will serve as a promising tool for splice sites prediction to facilitate genomic research.