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Retrieve UniProt Natural Variants by Sequence Position

Source: R/uniprot_proteins.R
rba_uniprot_variation_locations.Rd

Retrieve natural variants annotated at specified amino-acid positions in UniProt protein sequences. Each supplied accession is paired with the corresponding element of locations.

Usage

rba_uniprot_variation_locations(accession, locations, save_peff = FALSE, ...)

Arguments

accession

Character: UniProtKB accession(s). You can supply up to 100 accessions. Each accession is paired with the corresponding element of locations.

locations

Character or Numeric: Amino-acid position(s) within each protein sequence. Each element should be a positive whole number or a character string of comma-separated positions, such as "5,7". You can supply up to 100 elements, and their number should equal the number of supplied accessions.

save_peff

Logical or Character: (default = FALSE)

  • FALSE: Return the parsed JSON response.

  • TRUE: Save the PEFF response to an automatically generated path.

  • Character string: A valid file path to save the PEFF file.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

With save_peff = FALSE, a list named by UniProt accession. Each element contains entry metadata, the protein sequence, and matching variants in its features element. Repeated groups for the same accession are combined by the API, and features can be empty when no variant is annotated at the requested positions. Otherwise, the PEFF response is written to disk and returned as a character string.

Details

A locations element can specify one position or several comma-separated positions. The returned records are grouped by UniProt accession and include the protein sequence and variant annotations found at the requested positions.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/variation/accession_locations/{accession_locations}"

References

  • The UniProt Consortium. (2025). UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research, 53(D1), D609–D617. https://doi.org/10.1093/nar/gkae1010

  • Nightingale, A., Antunes, R., Alpi, E., Bursteinas, B., Gonzales, L., Liu, W., Luo, J., Qi, G., Turner, E., & Martin, M. (2017). The Proteins API: Accessing key integrated protein and genome information. Nucleic Acids Research, 45(W1), W539–W544. https://doi.org/10.1093/nar/gkx237

  • Proteins API Documentation

  • Citations note on UniProt website

See also

Other "UniProt - Variation": rba_uniprot_variation(), rba_uniprot_variation_search()

Examples

# \donttest{
rba_uniprot_variation_locations(
    accession = c("P05067", "Q99616"),
    locations = c("5,7", "5,29"))
# }