alphagenome_predictor
Predict regulatory effects of genetic variants on gene expression, chromatin accessibility, splicing, and promoter activity using AlphaGenome. Requires an API key and integration with BioMCP for variant interpretation.
Instructions
Predict variant effects on gene regulation using Google DeepMind's AlphaGenome.
⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your analysis strategy!
AlphaGenome provides state-of-the-art predictions for how genetic variants
affect gene regulation, including:
- Gene expression changes (RNA-seq)
- Chromatin accessibility impacts (ATAC-seq, DNase-seq)
- Splicing alterations
- Promoter activity changes (CAGE)
This tool requires:
1. AlphaGenome to be installed (see error message for instructions)
2. An API key from https://deepmind.google.com/science/alphagenome
API Key Options:
- Provide directly via the api_key parameter
- Or set ALPHAGENOME_API_KEY environment variable
Example usage:
- Predict regulatory effects of BRAF V600E mutation: chr7:140753336 A>T
- Assess non-coding variant impact on gene expression
- Evaluate promoter variants in specific tissues
Note: This is an optional tool that enhances variant interpretation
with AI predictions. Standard annotations remain available via variant_getter.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| alternate | Yes | Alternate allele(s) (e.g., 'T', 'A') | |
| api_key | No | AlphaGenome API key. Check if user mentioned 'my AlphaGenome API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one. | |
| chromosome | Yes | Chromosome (e.g., 'chr7', 'chrX') | |
| interval_size | No | Size of genomic interval to analyze in bp (max 1,000,000) | |
| position | Yes | 1-based genomic position of the variant | |
| reference | Yes | Reference allele(s) (e.g., 'A', 'ATG') | |
| significance_threshold | No | Threshold for significant log2 fold changes (default: 0.5) | |
| tissue_types | No | UBERON ontology terms for tissue-specific predictions (e.g., 'UBERON:0002367' for external ear) |
Input Schema (JSON Schema)
{
"properties": {
"alternate": {
"description": "Alternate allele(s) (e.g., 'T', 'A')",
"title": "Alternate",
"type": "string"
},
"api_key": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "AlphaGenome API key. Check if user mentioned 'my AlphaGenome API key is...' in their message. If not provided here and no env var is set, user will be prompted to provide one.",
"title": "Api Key"
},
"chromosome": {
"description": "Chromosome (e.g., 'chr7', 'chrX')",
"title": "Chromosome",
"type": "string"
},
"interval_size": {
"default": 131072,
"description": "Size of genomic interval to analyze in bp (max 1,000,000)",
"maximum": 1000000,
"minimum": 2000,
"title": "Interval Size",
"type": "integer"
},
"position": {
"description": "1-based genomic position of the variant",
"title": "Position",
"type": "integer"
},
"reference": {
"description": "Reference allele(s) (e.g., 'A', 'ATG')",
"title": "Reference",
"type": "string"
},
"significance_threshold": {
"default": 0.5,
"description": "Threshold for significant log2 fold changes (default: 0.5)",
"maximum": 5,
"minimum": 0,
"title": "Significance Threshold",
"type": "number"
},
"tissue_types": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "UBERON ontology terms for tissue-specific predictions (e.g., 'UBERON:0002367' for external ear)",
"title": "Tissue Types"
}
},
"required": [
"chromosome",
"position",
"reference",
"alternate"
],
"title": "alphagenome_predictorArguments",
"type": "object"
}