> ## 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 junction score > Score whether AlphaGenome splice junction predictions align to requested donor/acceptor positions.

**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.

Tools Used Tools Used Source Source Cite Cite

Go to Tool Page

evo-design/proto-language/proto\_language/constraint/rna\_splicing/alphagenome\_splice\_junction.py

View source

```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} } ```

Copy citation

Constraint contributors

Score splice-junction support at configured donor/acceptor positions. ## API Reference

ConfigAlphaGenomeSpliceJunctionConfig Source

Configuration for AlphaGenome splice-junction scoring. Genomic context sequence for cassette integration. Left flanking cassette context. Right flanking cassette context. AlphaGenome ontology term(s) to score. 0-based donor position in left\_flank + intron\_core + right\_flank. 0-based acceptor position in left\_flank + intron\_core + right\_flank. 'max' rewards junction support; 'min' penalizes it. Options: `max`, `min` Track strand subset to aggregate. Options: `positive`, `negative`, `all` AlphaGenome model version. Organism for AlphaGenome prediction. Options: `human`, `mouse` Device for AlphaGenome prediction. Timeout in seconds for AlphaGenome prediction.

## Usage ```python python icon="python" theme={null} from proto_language.core import Constraint from proto_language.constraint import alphagenome_splice_junction_constraint, AlphaGenomeSpliceJunctionConfig constraint = Constraint( inputs=[segment], function=alphagenome_splice_junction_constraint, function_config=AlphaGenomeSpliceJunctionConfig( # Configure parameters here ), ) scores = constraint.evaluate() ``` ## Metadata | Property | Value | | --------------- | ---------------------------------------- | | Key | `alphagenome-splice-junction` | | Function | `alphagenome_splice_junction_constraint` | | Category | `rna_splicing` | | Mode | `discrete` | | Uses GPU | `True` | | Supported Types | `dna` |