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Map Genomic Coordinates to Protein Sequence Positions

Source: R/uniprot_coordinates.R
rba_uniprot_coordinates_location_genome.Rd

Map a genomic position or range within a chromosome and taxon to the corresponding UniProt protein sequence locations. A genomic location may match multiple proteins, isoforms, or transcript mappings. Supply g_position alone, or supply g_start and g_end together.

Usage

rba_uniprot_coordinates_location_genome(
  taxid,
  chromosome,
  g_position = NULL,
  g_start = NULL,
  g_end = NULL,
  ...
)

Arguments

taxid

Numeric: NIH-NCBI Taxon ID.

chromosome

Character or Numeric: Chromosome name, e.g. 1, 20, or X.

g_position

Numeric: (optional) Genomic position. Supply this alone, or supply both g_start and g_end.

g_start

Numeric: (optional) Genomic range start.

g_end

Numeric: (optional) Genomic range end.

...

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

Value

A list with a locations element containing the matching UniProt protein and genomic mappings. Records can include protein positions, amino acids, transcript and translation identifiers, chromosome, strand, genome assembly, and mapped sequence features.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/coordinates/glocation/{taxonomy}/{chromosome}:{gPosition}"
"GET https://www.ebi.ac.uk/proteins/api/coordinates/glocation/{taxonomy}/{chromosome}:{gStart}-{gEnd}"

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(), rba_uniprot_coordinates_location_protein(), rba_uniprot_coordinates_search()

Examples

# \donttest{
 rba_uniprot_coordinates_location_genome(
 taxid = 9606, chromosome = 11, g_position = 36573305)
# }