> ## Documentation Index
> Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt
> Use this file to discover all available pages before exploring further.
# AlphaGenome Interval Track
> Score AlphaGenome track signal over one or more intervals by minimizing or maximizing mean value.
**License:** AlphaGenome uses Apache-2.0 for code and Custom (AlphaGenome Terms of Use) for model weights and has restrictions around commercial use and may require explicit attribution when utilized. Model weights are gated and require accepting the provider's terms and authenticating with a HuggingFace token. Please refer to the [code license](https://github.com/google-deepmind/alphagenome_research/blob/main/LICENSE) and [model weights license](https://deepmind.google.com/science/alphagenome/model-terms) for full terms.
This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.
```bibtex theme={null}
@article{avsec2026alphagenome,
title={Advancing regulatory variant effect prediction with AlphaGenome},
author={Avsec, {\v{Z}}iga and Latysheva, Natasha and Cheng, Jun and Novati, Guido and Taylor, Kyle R and Ward, Tom and Bycroft, Clare and Nicolaisen, Lauren and Arvaniti, Eirini and Pan, Joshua and Thomas, Raina and Dutordoir, Vincent and Perino, Matteo and De, Soham and Karollus, Alexander and Gayoso, Adam and Sargeant, Toby and Mottram, Anne and Wong, Lai Hong and Drot{\'a}r, Pavol and Kosiorek, Adam and Senior, Andrew and Tanburn, Richard and Applebaum, Taylor and Basu, Souradeep and Hassabis, Demis and Kohli, Pushmeet},
journal={Nature},
year={2026},
volume={649},
number={8099},
pages={1206--1218},
doi={10.1038/s41586-025-10014-0}
}
```
Configuration for interval track-value scoring with AlphaGenome.
0-based half-open intervals scored relative to the target segment.
DNA context placed upstream of the target segment before AlphaGenome prediction.
DNA context placed downstream of the target segment before AlphaGenome prediction.
Full sequence length submitted to AlphaGenome after context composition.
AlphaGenome ontology term(s) to score.
AlphaGenome output type to score.
Options: `ATAC`, `CAGE`, `DNASE`, `RNA_SEQ`, `CHIP_HISTONE`, `CHIP_TF`, `SPLICE_SITES`, `SPLICE_SITE_USAGE`, `SPLICE_JUNCTIONS`, `CONTACT_MAPS`, `PROCAP`
Keywords selecting individual tracks (e.g. \['H3K4me1']) from a bundled output; None = all tracks.
Whether to maximize or minimize the interval mean signal.
Options: `maximize`, `minimize`
Signal value where maximize-mode sigmoid has its inflection.
Scale for maximize-mode sigmoid transform.
Upper bound for minimize-mode linear score; values above are clipped.
Optional off-target cell-type term(s); when set, scores the target-vs-off-target signal margin.
Signal-difference (target - off-target) where the contrastive sigmoid has its inflection.
Scale for the contrastive-mode margin sigmoid transform.
AlphaGenome model version.
Organism for AlphaGenome prediction.
Options: `human`, `mouse`
Device for AlphaGenome prediction.
Timeout (seconds) for each AlphaGenome prediction call.
evo-design/proto-language/proto\_language/constraint/sequence\_annotation/alphagenome\_interval\_track\_constraint.py
