symbol
download an ortholog dataset by gene symbol
symbol
Name
datasets download ortholog symbol - download an ortholog dataset by gene symbol
Synopsis
datasets download ortholog symbol <gene_symbol> [flags]
Description
Download an ortholog dataset by gene symbol and taxon (species name or species-level NCBI Taxonomy ID). If no taxon is specified, data will be returned for human. Ortholog data is calculated by NCBI for vertebrates and insects. Ortholog data packages include gene, transcript and protein sequence, a data table and a data report. Datasets are downloaded as a zip file.
The default ortholog dataset includes the following files:
- gene.fna (gene sequences)
- rna.fna (transcript sequences)
- protein.faa (protein sequences)
- data_report.jsonl (data report with gene metadata)
- data_table.tsv (data table with gene metadata, one transcript per row)
- dataset_catalog.json (a list of files and file types included in the dataset)
Refer to NCBI’s download and install documentation for information about getting started with the command-line tools.
Examples
datasets download ortholog symbol tp53
datasets download ortholog symbol brca1 --taxon mouse
Options
--api-key string NCBI Datasets API Key
--exclude-gene exclude gene.fna (gene sequence file)
--exclude-protein exclude protein.faa (protein sequence file)
--exclude-rna exclude rna.fna (transcript sequence file)
--filename string specify a custom file name for the downloaded dataset (default "ncbi_dataset.zip")
-h, --help help for symbol
--include-3p-utr include 3p_utr.fna (3'-UTR sequence file)
--include-5p-utr include 5p_utr.fna (5'-UTR sequence file)
--include-cds include cds.fna (CDS sequence file)
--inputfile string read a list of gene symbols from a file to use as input
--no-progressbar hide progress bar
--taxon string specify a species name (common or scientific) or species-level NCBI Taxonomy ID (default "human")
--taxon-filter strings limit results to ortholog data for a specified taxonomic group
Generated March 11, 2025