> ## 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 splice site usage score
> Score splice-site usage with AlphaGenome on three segments (left_flank, intron_core, right_flank).
**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}
}
```
Score AlphaGenome SSU at selected positions in a three-part target.
Each input tuple contains three DNA sequences (left\_flank, intron\_core,
right\_flank) which are concatenated into a target, wrapped with cassette
contexts, and integrated into a genomic context for AlphaGenome prediction.
## API Reference
Configuration for AlphaGenome splice-site-usage scoring.
Takes three segments (left\_flank, intron\_core, right\_flank), concatenates
them into a target sequence, wraps with cassette contexts, and integrates
into a genomic context for AlphaGenome prediction. Splice positions are
specified relative to the concatenated target sequence.
Genomic context sequence for cassette integration (e.g., AAVS1 safe harbor locus).
Left flanking context for the cassette (plasmid/gene sequence 5' of the target).
Right flanking context for the cassette (plasmid/gene sequence 3' of the target).
AlphaGenome ontology term(s) to score.
0-indexed position(s) in the concatenated target to evaluate.
'max' returns 1-mean(SSU); 'min' returns mean(SSU).
Options: `max`, `min`
Score each splice position as the max usage within +/- this many positions; 0 = exact index.
Track strand subset to aggregate over.
Options: `positive`, `negative`, `all`
AlphaGenome model version.
Organism for AlphaGenome prediction.
Options: `human`, `mouse`
Device for AlphaGenome prediction.
Timeout (seconds) for each AlphaGenome prediction call.
ReturnsConstraintOutput
One result per input. `score` is in `[0.0, 1.0]`
(interpretation depends on direction). `metadata` carries the selected
tracks plus `alphagenome_splice_site_usage_raw` and `_score`.
evo-design/proto-language/proto\_language/constraint/rna\_splicing/alphagenome\_splice\_site\_usage.py
