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Get Genome coordinate by Protein Sequence position

Source: R/uniprot_coordinates.R
rba_uniprot_coordinates_sequence.Rd

Using this function you can retrieve genome coordinates of a given UniProt protein by providing protein position or position range. You can either supply 'p_position' alone or supply 'p_start' and 'p_end' together.

Usage

rba_uniprot_coordinates_sequence(
  accession,
  p_position = NULL,
  p_start = NULL,
  p_end = NULL,
  ...
)

Arguments

accession

UniProtKB primary or secondary accession.

p_position

(numeric) Protein sequence position

p_start

(numeric) Protein sequence position start

p_end

(numeric) Protein sequence 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/location /{accession}:{pPosition}"
"GET https://ebi.ac.uk/proteins/api/coordinates/location /{accession}:{pStart}-{pEnd}"

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_location(), rba_uniprot_coordinates_search()

Examples

# \donttest{
rba_uniprot_coordinates_sequence(accession = "P25942", p_position = 1)
# }
# \donttest{
rba_uniprot_coordinates_sequence(accession = "P25942",
    p_start = 1, p_end = 277)
# }