DeepMind’s AlphaGenome represents a powerful leap in decoding the non-coding “dark matter” of the human genome. Released in June 2025, this advanced AI model can analyze DNA sequences as long as 1 million base pairs, predicting regulatory activity with single-base precision—a breakthrough that overcomes the traditional trade-off between context breadth and resolution.
Ultra-long sequence analysis: AlphaGenome processes DNA stretches up to 1 Mb, far beyond prior models.
Base-level insights: It predicts gene start/end sites, RNA expression, chromatin structure, transcription factor binding, and splice junctions.
Unified model architecture: It merges convolutional neural networks (for local motifs) with transformers (for long-range dependencies) into one model.
State-of-the-art accuracy: AlphaGenome excels in 24 of 26 variant effect benchmarks using datasets like ENCODE, GTEx, and FANTOM5.
AlphaGenome quantifies how single DNA mutations can disrupt gene regulation, especially in non-coding regions responsible for gene expression control. This enables:
AlphaGenome is the first model to unify long-range genomic context, base-level precision, and high performance across diverse tasks. As DeepMind’s Pushmeet Kohli puts it: “For the first time, we have a single model that unifies long-range context, base-level precision and state-of-the-art performance across a whole spectrum of genomic tasks.”