AlphaGenome

AlphaGenome, launched by Google DeepMind on June 25, 2025, is a large-scale deep-learning system that predicts how DNA segments regulate gene expression and how single-nucleotide variants disrupt that regulation. It accepts up to one million base pairs of sequence and produces thousands of quantitative predictions across 11 modalities — gene expression, splicing, chromatin accessibility, histone marks, transcription factor binding, and 3D genome contacts — outperforming the best alternative models in 22 of 24 evaluated genome tracks. A September 2026 Atlas release precomputed predictions for all 9 billion possible human single-nucleotide variants.

Limitations: the API is free for non-commercial use only, with commercial access via Google Cloud listed as coming soon; predicting effects of mutations on genes more than 100,000 base pairs away remains difficult. Trained on human and mouse data, with untested effectiveness on other organisms.