Download an ortholog data package

Download an NCBI Datasets gene ortholog data package, including FASTA sequences and metadata

Download an ortholog data package

Download an NCBI Datasets gene ortholog data package, including FASTA sequences and metadata

Download a gene ortholog set as a zip-compressed NCBI Datasets gene data package. Currently, NCBI calculated ortholog sets are available for vertebrates and insects (as separate sets). Users can request NCBI ortholog sets by using the --ortholog flag under the datasets summary/download gene command.  

The --ortholog flag serves two purposes:

  • It explicitly requests an ortholog set for a gene-id, accession or symbol.
  • It defines the taxonomic scope of the ortholog set. The options are:
    • --ortholog all: returns the complete ortholog set available for the requested gene.
    • --ortholog <any taxon>: restricts the ortholog set to the specific taxonomic range.

Using Gene IDs

Download the Angiotensin Converting Enzyme 2 (ACE2) ortholog set for mammals.

datasets download gene gene-id 59272 --ortholog mammals

Using gene symbols

Download the complete ortholog set for the CF transmembrane conductance regulator (CFTR) gene.

datasets download gene symbol cftr --ortholog all

Using RefSeq transcript or protein accessions

Download the primate ortholog set for the CF transmembrane conductance regulator (CFTR) gene.

datasets download gene accession NM_000492.4 --ortholog primates
Generated February 26, 2025