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Search UniProt entries by taxonomy and genomic coordinates

Source: R/uniprot_coordinates.R
rba_uniprot_coordinates_location.Rd

For more information about how UniProt imports and calculates genomic coordinates data, see:
McGarvey, P. B., Nightingale, A., Luo, J., Huang, H., Martin, M. J., Wu, C., & 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

Usage

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

Arguments

taxid

NIH-NCBI Taxon ID.

locations

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

Only return proteins that are in range.

feature

(logical) Get features?

...

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

Value

a list containing UniProt proteins which match the supplied genomic location and taxonomy ID.

Corresponding API Resources

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

References

  • The UniProt Consortium, UniProt: the universal protein knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100

  • Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin, The Proteins API: accessing key integrated protein and genome information, Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W539–W544, https://doi.org/10.1093/nar/gkx237

  • Proteins API Documentation

  • Citations note on UniProt website

See also

Other "UniProt - Coordinates": rba_uniprot_coordinates(), rba_uniprot_coordinates_search(), rba_uniprot_coordinates_sequence()

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)
# }