Alphagenome Tools

Configuration File: alphagenome_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the alphagenome_tools.json configuration file.

Available Tools

AlphaGenome_predict_interval (Type: AlphaGenomeTool)

Predict multimodal genomic tracks for a genomic interval with DeepMind AlphaGenome (single DNA-se…

AlphaGenome_predict_interval tool specification

Tool Information:

  • Name: AlphaGenome_predict_interval

  • Type: AlphaGenomeTool

  • Description: Predict multimodal genomic tracks for a genomic interval with DeepMind AlphaGenome (single DNA-sequence model; up to 1 Mb at single-base resolution). Returns a compact per-modality summary (track counts and shapes) for the requested outputs. Hosted API via the alphagenome SDK; free for non-commercial use (set ALPHA_GENOME_API_KEY).

Parameters:

  • chromosome (string) (required) Chromosome, e.g. ‘chr19’.

  • start (integer) (required) Interval start (0-based).

  • end (integer) (required) Interval end.

  • output_types ([‘array’, ‘null’]) (optional) Modalities to predict, e.g. [‘RNA_SEQ’,’ATAC’] (default [‘RNA_SEQ’]).

  • ontology_terms ([‘array’, ‘null’]) (optional) Optional tissue/cell ontology terms (e.g. [‘UBERON:0001114’] = liver) to restrict tracks.

  • organism ([‘string’, ‘null’]) (optional) ‘human’ (default) or ‘mouse’.

  • sequence_length ([‘string’, ‘null’]) (optional) Context window: 16KB, 100KB, 500KB, or 1MB (default).

Example Usage:

query = {
    "name": "AlphaGenome_predict_interval",
    "arguments": {
        "chromosome": "example_value",
        "start": 10,
        "end": 10
    }
}
result = tu.run(query)

AlphaGenome_score_variant (Type: AlphaGenomeTool)

Score a regulatory variant’s effect with DeepMind AlphaGenome (Avsec, Nature 2026), the hosted su…

AlphaGenome_score_variant tool specification

Tool Information:

  • Name: AlphaGenome_score_variant

  • Type: AlphaGenomeTool

  • Description: Score a regulatory variant’s effect with DeepMind AlphaGenome (Avsec, Nature 2026), the hosted successor to Enformer/Borzoi. Predicts ref vs alt over up to 1 Mb at single-base resolution and returns the recommended per-track effect scores (sorted by |effect|). Hosted API via the alphagenome SDK; free for non-commercial use (set ALPHA_GENOME_API_KEY).

Parameters:

  • chromosome (string) (required) Chromosome, e.g. ‘chr22’.

  • position (integer) (required) 1-based variant position.

  • reference_bases (string) (required) Reference allele, e.g. ‘A’.

  • alternate_bases (string) (required) Alternate allele, e.g. ‘C’.

  • output_type ([‘string’, ‘null’]) (optional) Modality to score: RNA_SEQ (default), ATAC, DNASE, CAGE, CHIP_HISTONE, CHIP_TF, SPLICE_SITES, CONTACT_MAPS.

  • organism ([‘string’, ‘null’]) (optional) ‘human’ (default) or ‘mouse’.

  • sequence_length ([‘string’, ‘null’]) (optional) Context window: 16KB, 100KB, 500KB, or 1MB (default).

  • top_n ([‘integer’, ‘null’]) (optional) Number of top |effect| tracks to return (default 20).

Example Usage:

query = {
    "name": "AlphaGenome_score_variant",
    "arguments": {
        "chromosome": "example_value",
        "position": 10,
        "reference_bases": "example_value",
        "alternate_bases": "example_value"
    }
}
result = tu.run(query)