A multispecies foundation model for genome function prediction, gene annotation and sequence design

Nucleotide Transformer v3 (NTv3) is a long-context cross-kingdom foundation model that matches or exceeds published functional-track models across 19 species, using sequences up to 1Mb.

• Why it matters: Genomic models have not combined functional prediction, gene annotation, and controllable sequence design across many species, limiting comparative genomics and synthetic biology.
• What they did: NTv3 is pre-trained on more than 128,000 genomes and post-trained on 16,262 functional tracks across 15 animal and plant genomes, then evaluated via matched human assays and cross-species comparisons.
• The result: NTv3 improves track prediction with genome pre-training and expanded functional supervision, outperforms ab initio gene predictors with fewer spurious models and better long-gene recovery, and designs regulatory DNA with specific activity levels validated in plant and fly enhancers.