Expression, Regulatory Tracks and Contact Maps: parameters and notes

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

These functions call existing models or prediction services. Weights, SDKs, credentials and service terms remain provider requirements; DNAKit did not retrain these models.

Predict multimodal genomic tracks with AlphaGenome

dnakit.databases.alpha_genome_predict_interval(*, chromosome, start, end, output_types=None, ontology_terms=None, organism=None, sequence_length=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
chromosome	string	Required	Chromosome, e.g. 'chr19'.
start	integer	Required	Interval start (0-based).
end	integer	Required	Interval end.
output_types	array | null	None	Modalities to predict, e.g. ['RNA_SEQ','ATAC'] (default ['RNA_SEQ']). {"items": {"type": "string"}}
ontology_terms	array | null	None	Optional tissue/cell ontology terms (e.g. ['UBERON:0001114'] = liver) to restrict tracks. {"items": {"type": "string"}}
organism	string | null	None	'human' (default) or 'mouse'.
sequence_length	string | null	None	Context window: 16KB, 100KB, 500KB, or 1MB (default).
verbose	bool	True	Progress flag.

Configure before running: ALPHA_GENOME_API_KEY.