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Updated: Jun 1, 2026
A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data
Published on: September 25, 2021
DeepCas12a: a hybrid deep learning framework for accurate AsCas12a efficiency prediction from sequence and epigenetic
Yiming Shi1,2, Junkai Yin1,2, Shurui Ning1,2
1Department of Infectious Dermatosis, Center of Infectious Skin Diseases, Bioinformatics Department, School of Life Sciences and Technology, Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200092, China.
Abstract:
CRISPR-Cas12a (Cpf1) offers distinct advantages for genome editing due to its flexible, T-rich PAM recognition. However, variable cleavage efficiency-modulated by sequence context and epigenetic features-remains a challenge, with existing tools facing challenges in modeling the high-order interactions between multimodal features. Here, we present DeepCas12a, a hybrid deep learning framework integrating Convolutional Neural Networks (CNNs) and a Vision Transformer (ViT) encoder to capture both local sequence motifs and long-range dependencies. The model fuses DNA sequence data with epigenetic profiles (DNA methylation and chromatin accessibility) in an end-to-end architecture. Benchmarked on an independent test set, DeepCas12a outperformed state-of-the-art predictors, achieving an Average Precision of 0.783, an AUC of 0.868, and a Spearman correlation of 0.630. Furthermore, interpretability analysis via saliency maps confirms the model captures biologically relevant features, including PAM specificity and seed region sensitivity, facilitating rational guide RNA design.