geneML: Gene annotation across diverse fungal species using deep learning (opens in new tab)

Accurate gene prediction remains a major bottleneck in fungal genomics, where lineage diversity and alternative splicing challenge existing ab initio methods. Here, we present geneML, a deep learning-based gene prediction tool tailored to fungal genomes. Across nine reference genomes spanning diverse fungal taxa, geneML improved gene-level F1 score from 64.9 to 67.1 compared to BRAKER3 with protein-based hints, driven by substantially higher recall (69.0 vs. 64.1) at equivalent precision. gen...