Predicting DNA sequence splice site based on graph convolutional network and DNA graph construction

Abstract

Identifying splice sites is essential for gene structure analysis and eukaryotic genome annotation. Recently, computational and deep learning approaches for splice site detection have advanced, focusing on reducing false positives by distinguishing true from pseudo splice sites. This paper introduces GraphSplice, a method using graph convolutional neural networks. It encodes DNA sequences into directed graphs to extract features and predict splice sites. Tested across multiple datasets, GraphSplice consistently achieved high accuracy (91%-94%) and F1Scores (92%-94%), outperforming state-of-the-art models by up to 9.16% for donors and 5.64% for acceptors. Cross-species experiments also show GraphSplice’s capability to annotate splice sites in under-trained genomic datasets, proving its wide applicability as a tool for DNA splice site analysis.