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Get Genome coordinate by Gene Sequence position

Source: R/uniprot_coordinates.R
rba_uniprot_coordinates_location_genome.Rd

Using this function you can retrieve genome coordinates of a given UniProt protein by providing Genome location position or range. You can either 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

NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

chromosome

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

g_position

(numeric) Genome location position

g_start

(numeric) Genome location position start

g_end

(numeric) Genome location position end

...

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

Value

Genome coordinates of your supplied proteins.

Details

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

Corresponding API Resources

"GET https://ebi.ac.uk/proteins/api/coordinates/glocation /{accession}:{pPosition}"
"GET https://ebi.ac.uk/proteins/api/coordinates/glocation /{accession}:{pStart}-{pEnd}"

References

  • The UniProt Consortium , UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010, https://doi.org/10.1093/nar/gkae1010

  • 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_location(), rba_uniprot_coordinates_location_protein(), rba_uniprot_coordinates_search()

Examples

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