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AlphaGenome splice site usage score
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 and model weights license for full terms.

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evo-design/proto-language/proto_language/constraint/rna_splicing/alphagenome_splice_site_usage.py
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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.

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API Reference

ConfigAlphaGenomeSpliceSiteUsageConfig Source
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.
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string
required
Genomic context sequence for cassette integration (e.g., AAVS1 safe harbor locus).
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string
required
Left flanking context for the cassette (plasmid/gene sequence 5’ of the target).
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string
required
Right flanking context for the cassette (plasmid/gene sequence 3’ of the target).
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List[string]
required
AlphaGenome ontology term(s) to score.
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List[integer]
required
0-indexed position(s) in the concatenated target to evaluate.
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enum
default:"max"
‘max’ returns 1-mean(SSU); ‘min’ returns mean(SSU).Options: max, min
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integer
default:"0"
Score each splice position as the max usage within +/- this many positions; 0 = exact index.
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enum
default:"positive"
Track strand subset to aggregate over.Options: positive, negative, all
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string
default:"all_folds"
AlphaGenome model version.
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enum
default:"human"
Organism for AlphaGenome prediction.Options: human, mouse
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string
default:"cuda"
Device for AlphaGenome prediction.
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integer
default:"3600"
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.

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Usage

python

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Metadata