Understanding the Impact of Individual Nucleotide on Oxford Nanopore Current Signals With Interpretable Prediction Models.

ABSTRACT: Oxford nanopore sequencing enabled real-time, long-read analysis of DNA by detecting ionic current signals associated with K-mer sequences. Although many studies analyzed sequence and modification detection, our understanding of how multiple nucleotides of the K-mer sequence determine nanopore signals together is still limited. In this study, we seek to unveil the positional impact of individual nucleotide through interpretable prediction models. Multiple machine learning models were trained and optimized. To increase model interpretability and explore underlying mechanisms, the tool of SHapley Additive exPlanations was applied to make an assessment of both nucleotides and positions. Our results show that previously unseen Oxford nanopore signals were accurately predicted, and results were

SUBMITTER: Wang Y 

PROVIDER: S-EPMC12457769 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature