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Get UniProt protein sequence features by accession

Source: R/uniprot_proteins.R
rba_uniprot_features.Rd

Use this function to retrieve sequence annotations (features) of a protein by it's UniProt accession.

Usage

rba_uniprot_features(accession, types = NULL, categories = NULL, ...)

Arguments

accession

UniProtKB primary or secondary accession.

types

Sequence annotation (Features) types. accepted values are: "INIT_MET", "SIGNAL", "PROPEP", "TRANSIT", "CHAIN", "PEPTIDE", "TOPO_DOM", "TRANSMEM", "DOMAIN", "REPEAT", "CA_BIND", "ZN_FING", "DNA_BIND", "NP_BIND", "REGION", "COILED", "MOTIF", "COMPBIAS", "ACT_SITE", "METAL", "BINDING", "SITE", "NON_STD", "MOD_RES", "LIPID", "CARBOHYD", "DISULFID", "CROSSLNK", "VAR_SEQ", "VARIANT", "MUTAGEN", "UNSURE", "CONFLICT", "NON_CONS", "NON_TER", "HELIX", "TURN", "STRAND" and/or "INTRAMEM". You can supply up to 20 types.

categories

Sequence annotation (Features) categories (subsection). accepted values are: "MOLECULE_PROCESSING", "TOPOLOGY", "SEQUENCE_INFORMATION", "STRUCTURAL", "DOMAINS_AND_SITES", "PTM", "VARIANTS" and/or "MUTAGENESIS". You can supply up to 8 categories.

...

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

Value

A list in which you can find all of your given protein's sequence annotations in a sub-list named "features".

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/features/{accession}"

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 - Features": rba_uniprot_features_search()

Examples

# \donttest{
rba_uniprot_features("Q99616")
# }
# \donttest{
rba_uniprot_features(accession = "Q99616", types = "DISULFID")
# }