MEHunter: transformer-based mobile element variant detection from long reads.

ABSTRACT:

Summary

Mobile genetic elements (MEs) are heritable mutagens that significantly contribute to genetic diseases. The advent of long-read sequencing technologies, capable of resolving large DNA fragments, offers promising prospects for the comprehensive detection of ME variants (MEVs). However, achieving high precision while maintaining recall performance remains challenging mainly brought by the variable length and similar content of MEV signatures, which are often obscured by the noise in long reads. Here, we propose MEHunter, a high-performance MEV detection approach utilizing a fine-tuned transformer model adept at identifying potential MEVs with fragmented features. Benchmark experiments on both simulated and real datasets demonstrate that MEHunter consistently achieves higher a

SUBMITTER: Jiang T 

PROVIDER: S-EPMC11415824 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature