Extended Data Fig. 3: Nucleotide-level performance comparison with evidence-assisted annotation pipelines across 12 model species. | Nature Methods

Extended Data Fig. 3: Nucleotide-level performance comparison with evidence-assisted annotation pipelines across 12 model species.

From: Highly accurate ab initio gene annotation with ANNEVO

Extended Data Fig. 3: Nucleotide-level performance comparison with evidence-assisted annotation pipelines across 12 model species.

ANNEVO achieved the highest mean F1 score (0.92), driven by its superior recall (0.922), indicating more complete coding region identification. BRAKER3 exhibited slightly lower precision (0.906 vs. 0.919 for ANNEVO) and its completeness was substantially lower (recall: 0.805 vs. 0.922 for ANNEVO). The 7% absolute improvement in F1 by ANNEVO reflects its optimized balance between precision and recall, surpassing evidence-dependent methods despite its relying solely on genomic sequence inputs.

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