原始 DNA 的基因名称与区间注释：参数与补充说明¶

用法和示例见功能教程。

各功能按作用、API、输入、输出、示例代码和结果说明介绍。运行前按说明准备凭据、本地文件与可选依赖；远程结果随数据库版本与查询时间变化。

查询基因家族的跨物种系统发育树¶

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

参数	类型	必填 / 默认值	说明与约束
`gene`	string	必填	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	运行提示开关。

查询跨物种直系同源基因¶

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

参数	类型	必填 / 默认值	说明与约束
`gene`	string	必填	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	运行提示开关。

查询基因复制产生的旁系同源基因¶

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

参数	类型	必填 / 默认值	说明与约束
`gene`	string	必填	Gene symbol or Ensembl gene ID. Examples: 'TP53', 'BRCA1', 'ENSG00000141510'.
`species`	string	None	Species (default: 'human'). Examples: 'human', 'mouse', 'zebrafish'.
`verbose`	bool	True	运行提示开关。

按基因名称查询同源关系¶

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

参数	类型	必填 / 默认值	说明与约束
`species`	string	必填	Source species (e.g., 'human', 'homo_sapiens')
`symbol`	string	必填	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	运行提示开关。

查询基因组区间重叠的注释特征¶

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

参数	类型	必填 / 默认值	说明与约束
`species`	string	必填	Species (e.g., 'human', 'homo_sapiens')
`region`	string	必填	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	运行提示开关。

查询基因组区间内的调控元件¶

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

参数	类型	必填 / 默认值	说明与约束
`region`	string	必填	Genomic region in format 'chromosome:start-end' (e.g., '1:1000000-2000000')
`species`	string	None	Species name (default 'human')
`feature`	string	必填	Feature type (must be 'regulatory' for this tool)
`verbose`	bool	True	运行提示开关。

按编号或名称查询 Ensembl 基因信息¶

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

参数	类型	必填 / 默认值	说明与约束
`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	运行提示开关。

按官方基因名称查询 HGNC 注释¶

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

参数	类型	必填 / 默认值	说明与约束
`symbol`	string	必填	Official HGNC gene symbol. Examples: 'TP53', 'BRCA1', 'EGFR', 'INS', 'ACE2'.
`verbose`	bool	True	运行提示开关。

批量查询基因注释与标识映射¶

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

参数	类型	必填 / 默认值	说明与约束
`gene_ids`	array	必填	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	运行提示开关。

按基因编号获取综合注释¶

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

参数	类型	必填 / 默认值	说明与约束
`gene_id`	string	必填	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	运行提示开关。

按关键词或标识检索基因¶

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

参数	类型	必填 / 默认值	说明与约束
`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	运行提示开关。

按 NCBI Gene ID 获取基因详情¶

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

参数	类型	必填 / 默认值	说明与约束
`gene_id`	string	必填	NCBI Gene ID (numeric). Examples: '7157' (TP53), '672' (BRCA1), '3630' (INS), '22059' (mouse Trp53).
`verbose`	bool	True	运行提示开关。

按基因名称与物种查询 NCBI 基因¶

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

参数	类型	必填 / 默认值	说明与约束
`symbol`	string	必填	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	运行提示开关。

按 NCBI 基因编号查询直系同源基因¶

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

参数	类型	必填 / 默认值	说明与约束
`gene_id`	string	必填	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	运行提示开关。

获取 NCBI 基因摘要与功能信息¶

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

参数	类型	必填 / 默认值	说明与约束
`id`	string	必填	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	运行提示开关。

按物种和关键词检索 NCBI 基因编号¶

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

参数	类型	必填 / 默认值	说明与约束
`term`	string	必填	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	运行提示开关。

查询 MANE 转录本与 RefSeq 对应关系¶

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

参数	类型	必填 / 默认值	说明与约束
`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	运行提示开关。

查询 Ensembl 转录本历史记录¶

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

参数	类型	必填 / 默认值	说明与约束
`stable_id`	string	必填	Ensembl transcript stable id, e.g. 'ENST00000380152' (version optional).
`verbose`	bool	True	运行提示开关。

查询基因的转录本与 MANE 注释¶

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

参数	类型	必填 / 默认值	说明与约束
`gene_symbol`	string	必填	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	运行提示开关。