PlantGeneAnn-v2-Bryophyta

PlantGeneAnn

PlantGeneAnn (Plant Gene Annotator) is a tool for accurate ab initio protein-coding gene structure annotation in plant genomes. It automatically predicts nucleotide-level gene states on both genomic strands using a genome foundation model (GFM) and converts these predictions into biologically valid gene models through semi-Markov model (SMM) decoding. PlantGeneAnn-v2-Bryophyta is the pretrained model tailored for mosses, liverworts, and hornworts.

Developed by: hu-lab

Model and Pipeline Sources

• Model Checkpoint: PlantGeneAnn-v2-Bryophyta
• GitHub: https://github.com/qzzhang0131/PlantGeneAnn (Full annotation pipeline)

BibTeX Entry and Citation Info

@article{zhang2026plantgeneann,
  title={PlantGeneAnn: a high-accuracy ab initio plant gene annotation tool fine-tuned from a genome foundation model},
  author={Zhang, Qizhe and Zhang, Zhengyang and Lin, Kepeng and Wang, Jing and Deng, Kaixuan and Xu, Wei and Yang, Qing-Yong and Hu, Xuehai},
  journal={bioRxiv},
  year={2026},
  doi={10.64898/2026.06.25.733695},
  url={https://www.biorxiv.org/content/10.64898/2026.06.25.733695v2}
}