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Search UniProt entries by taxonomy and genomic coordinates

Source: R/uniprot_coordinates.R
rba_uniprot_coordinates_location.Rd

Retrieve UniProt entries or mapped protein features for a taxon and supplied genomic coordinates.

Usage

rba_uniprot_coordinates_location(
  taxid,
  locations,
  in_range = TRUE,
  feature = FALSE,
  ...
)

Arguments

taxid

Numeric: NIH-NCBI Taxon ID.

locations

Character: Genomic location formatted as chromosome:start-end. (e.g. "Y:17100001-19600000"). If you omit chromosome, it will be interpreted as any chromosome (e.g. "1-10000").

in_range

Logical: (default = TRUE) If TRUE, return only proteins that are fully contained in the supplied range.

feature

Logical: (default = FALSE) If TRUE, return mapped protein features rather than protein coordinate records.

...

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

Value

A list containing UniProt proteins that match the supplied genomic location and taxonomy ID.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/coordinates/{taxonomy}/{locations}/feature"
"GET https://www.ebi.ac.uk/proteins/api/coordinates/{taxonomy}/{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

  • McGarvey, P. B., Nightingale, A., Luo, J., Huang, H., Martin, M. J., Wu, C., & The UniProt Consortium. (2019). UniProt genomic mapping for deciphering functional effects of missense variants. Human Mutation, 40(6), 694–705. https://doi.org/10.1002/humu.23738

  • Proteins API Documentation

  • Citations note on UniProt website

See also

Other "UniProt - Coordinates": rba_uniprot_coordinates(), rba_uniprot_coordinates_location_genome(), rba_uniprot_coordinates_location_protein(), rba_uniprot_coordinates_search()

Examples

# \donttest{
rba_uniprot_coordinates_location(taxid = 9606,
    locations = "Y:17100001-19600000", in_range = TRUE)
# }
# \donttest{
rba_uniprot_coordinates_location(taxid = 9606,
    locations = "20:39000001", in_range = FALSE)
# }