Gene names and intervals from genomic DNA: 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.

Retrieve a cross-species gene family tree¶

dnakit.databases.ensembl_compara_get_gene_tree(*, gene, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	Required	Gene symbol or Ensembl gene ID. Examples: 'TP53', 'BRCA1', 'ENSG00000141510'. Ensembl IDs are more reliable than symbols for gene tree retrieval.
`species`	string	None	Species (default: 'human'). Used when providing a gene symbol. Examples: 'human', 'mouse'.
`verbose`	bool	True	Progress flag.

Retrieve orthologous genes across species¶

dnakit.databases.ensembl_compara_get_orthologues(*, gene, species=None, target_species=None, target_taxon=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	Required	Gene symbol or Ensembl gene ID. Examples: 'BRCA1', 'TP53', 'ENSG00000141510', 'ENSG00000012048'.
`species`	string	None	Source species (default: 'human'). Examples: 'human', 'mouse', 'zebrafish', 'drosophila_melanogaster'.
`target_species`	string	None	Target species to limit orthologue search. Examples: 'mouse', 'zebrafish', 'rat', 'drosophila_melanogaster'. Default: all species.
`target_taxon`	integer	None	NCBI taxon ID to limit orthologue search. Examples: 10090 (mouse), 7955 (zebrafish), 7227 (fruit fly). Alternative to target_species.
`verbose`	bool	True	Progress flag.

Retrieve paralogous genes¶

dnakit.databases.ensembl_compara_get_paralogues(*, gene, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	Required	Gene symbol or Ensembl gene ID. Examples: 'TP53', 'BRCA1', 'ENSG00000141510'.
`species`	string	None	Species (default: 'human'). Examples: 'human', 'mouse', 'zebrafish'.
`verbose`	bool	True	Progress flag.

Retrieve gene homology by symbol¶

dnakit.databases.ensembl_get_homology(*, species, symbol, target_species=None, target_taxon=None, type=None, sequence=None, aligned=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`species`	string	Required	Source species (e.g., 'human', 'homo_sapiens')
`symbol`	string	Required	Gene symbol (e.g., 'BRCA2', 'TP53')
`target_species`	string	None	Target species to find homologues in (optional, e.g., 'mouse', 'mus_musculus'). Leave empty to search all species.
`target_taxon`	string	None	Target taxonomic group (optional, e.g., 'Mammalia', 'Primates')
`type`	string	None	Homology type: 'orthologues' (different species), 'paralogues' (same species), 'all' (both)
`sequence`	string	None	Include sequences in response
`aligned`	boolean	None	Return aligned sequences
`verbose`	bool	True	Progress flag.

Retrieve annotations overlapping a genomic interval¶

dnakit.databases.ensembl_get_overlap_features(*, species, region, feature=None, biotype=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`species`	string	Required	Species (e.g., 'human', 'homo_sapiens')
`region`	string	Required	Genomic region (e.g., '7:140424943-140624564')
`feature`	string	None	Feature type to retrieve
`biotype`	string	None	Filter by biotype (optional, e.g., 'protein_coding', 'lincRNA', 'miRNA')
`verbose`	bool	True	Progress flag.

Retrieve regulatory features in a genomic interval¶

dnakit.databases.ensembl_get_regulatory_features(*, region, species=None, feature, verbose=True)

Parameter	Type	Required / default	Description and constraints
`region`	string	Required	Genomic region in format 'chromosome:start-end' (e.g., '1:1000000-2000000')
`species`	string	None	Species name (default 'human')
`feature`	string	Required	Feature type (must be 'regulatory' for this tool)
`verbose`	bool	True	Progress flag.

Look up Ensembl genes by identifier or symbol¶

dnakit.databases.ensembl_lookup_gene(*, gene_id=None, species=None, id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_id`	string	None	Ensembl gene ID or symbol (e.g., 'ENSG00000139618' or 'BRCA1'). If using a stable ID, the tool will automatically route to /lookup/id endpoint.
`species`	string	None	Species name required for gene symbols (default 'homo_sapiens'). Examples: 'homo_sapiens', 'mus_musculus', 'rattus_norvegicus'
`id`	string	None	DNAKit optional alias for gene_id
`verbose`	bool	True	Progress flag.

Retrieve HGNC annotations by official gene symbol¶

dnakit.databases.hgnc_fetch_gene_by_symbol(*, symbol, verbose=True)

Parameter	Type	Required / default	Description and constraints
`symbol`	string	Required	Official HGNC gene symbol. Examples: 'TP53', 'BRCA1', 'EGFR', 'INS', 'ACE2'.
`verbose`	bool	True	Progress flag.

Batch-query gene annotations and identifier mappings¶

dnakit.databases.my_gene_batch_query(*, gene_ids, species=None, fields=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_ids`	array	Required	List of gene IDs to query. Can mix different ID types (Entrez, Ensembl, symbols). {"items": {"type": "string"}}
`species`	string	None	Species filter for the query.
`fields`	string	None	Comma-separated list of fields to return for each gene.
`verbose`	bool	True	Progress flag.

Retrieve comprehensive annotations for a gene identifier¶

dnakit.databases.my_gene_get_gene_annotation(*, gene_id, fields=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_id`	string	Required	Gene ID to query. Can be Entrez Gene ID (e.g., '1017' for CDK2) or Ensembl ID (e.g., 'ENSG00000123374').
`fields`	string	None	Comma-separated list of fields to return. Available fields include: symbol, name, summary, go (gene ontology), pathway (KEGG/Reactome), interpro (protein domains), generif (gene references), pdb, uniprot.
`verbose`	bool	True	Progress flag.

Search genes by keyword or identifier¶

dnakit.databases.my_gene_query_genes(*, query=None, species=None, fields=None, size=None, q=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`query`	string	None	Search query. Can be gene symbol (e.g., 'CDK2'), name ('cyclin dependent kinase'), Entrez ID ('1017'), or Ensembl ID ('ENSG00000123374'). Supports wildcards (*) and boolean operators (AND, OR, NOT).
`species`	string	None	Species filter. Use common name or NCBI taxonomy ID. Examples: 'human', 'mouse', '9606' (human), 'all'.
`fields`	string	None	Comma-separated list of fields to return. Common fields: symbol, name, entrezgene, ensembl.gene, summary, go, pathway, interpro.
`size`	integer	None	Maximum number of results to return (1-100).
`q`	string	None	DNAKit optional alias for query
`verbose`	bool	True	Progress flag.

Retrieve gene details by NCBI Gene ID¶

dnakit.databases.ncbidatasets_get_gene(*, gene_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_id`	string	Required	NCBI Gene ID (numeric). Examples: '7157' (TP53), '672' (BRCA1), '3630' (INS), '22059' (mouse Trp53).
`verbose`	bool	True	Progress flag.

Look up NCBI genes by symbol and organism¶

dnakit.databases.ncbidatasets_get_gene_by_symbol(*, symbol, taxon=None, organism=None, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`symbol`	string	Required	Gene symbol. Examples: 'TP53', 'BRCA1', 'INS', 'EGFR'. {"minLength": 1, "pattern": ".\S."}
`taxon`	string	None	Organism as common name or taxonomy ID. Examples: 'human', 'mouse', 'rat', '9606', '10090'. Default: 'human' (reported as metadata.query_taxon_defaulted). Synonyms `organism` and `species` are accepted. {"minLength": 1, "pattern": ".\S."}
`organism`	string	None	Synonym for `taxon`. Used when `taxon` is not supplied. {"minLength": 1, "pattern": ".\S."}
`species`	string	None	Synonym for `taxon`. Used when neither `taxon` nor `organism` is supplied. {"minLength": 1, "pattern": ".\S."}
`verbose`	bool	True	Progress flag.

Retrieve orthologs for an NCBI Gene ID¶

dnakit.databases.ncbidatasets_get_orthologs(*, gene_id, page_size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_id`	string	Required	NCBI Gene ID (numeric). Examples: '7157' (TP53), '672' (BRCA1), '3630' (INS).
`page_size`	integer	None	Maximum number of orthologs to return (1-100). Default: 20.
`verbose`	bool	True	Progress flag.

Retrieve NCBI gene summaries and functional information¶

dnakit.databases.ncbigene_get_summary(*, id, verbose=True)

Parameter	Type	Required / default	Description and constraints
`id`	string	Required	NCBI Gene ID (Entrez Gene ID). Can be a single ID or comma-separated list. Examples: '7157' (TP53), '672' (BRCA1), '1956' (EGFR), '3845' (KRAS). Get IDs from NCBIGene_search.
`verbose`	bool	True	Progress flag.

Search NCBI Gene IDs by organism and keyword¶

dnakit.databases.ncbigene_search(*, term, retmax=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`term`	string	Required	Search query. Use gene symbol with organism filter for best results. Format: 'GENE[Symbol] AND Organism[Organism]'. Examples: 'TP53[Symbol] AND Homo sapiens[Organism]', 'BRCA1[Symbol] AND Homo sapiens[Organism]', 'insulin AND Homo sapiens[Organism]', 'EGFR AND Mus musculus[Organism]'.
`retmax`	integer	None	Maximum number of results to return (default 10, max 100).
`verbose`	bool	True	Progress flag.

Retrieve MANE transcripts and RefSeq mappings¶

dnakit.databases.tark_get_mane_transcripts(*, gene=None, ensembl_id=None, refseq_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string \| null	None	HGNC gene symbol, e.g. 'BRCA2', 'CFTR'.
`ensembl_id`	string \| null	None	Ensembl transcript id, e.g. 'ENST00000380152' (version optional).
`refseq_id`	string \| null	None	RefSeq transcript id, e.g. 'NM_000059' (version optional).
`verbose`	bool	True	Progress flag.

Retrieve archived Ensembl transcript records¶

dnakit.databases.tark_get_transcript(*, stable_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
`stable_id`	string	Required	Ensembl transcript stable id, e.g. 'ENST00000380152' (version optional).
`verbose`	bool	True	Progress flag.

Retrieve gene transcripts and MANE annotations¶

dnakit.databases.variant_validator_gene2transcripts(*, gene_symbol, gene=None, gene_name=None, transcript_set=None, genome_build=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_symbol`	string	Required	HGNC gene symbol (e.g., 'TP53', 'BRCA1', 'EGFR'). Aliases: gene, gene_name.
`gene`	string	None	Alias for gene_symbol.
`gene_name`	string	None	Alias for gene_symbol.
`transcript_set`	string	None	Transcript filter: 'mane' for MANE Select/Plus Clinical only, 'refseq' for RefSeq transcripts, 'ensembl' for Ensembl, 'all' for everything
`genome_build`	string	None	Reference genome assembly: 'GRCh37' or 'GRCh38' (default: GRCh38)
`verbose`	bool	True	Progress flag.