rba_uniprot_antigens_search {rbioapi}

Search Antigens in UniProt

Description

UniProt maps Antigenic (Antibody-binding) features from different sources to the proteins' sequences. Using this function, you can search for Antigenic sequences that has been map to UniProt proteins. You may also refine your search with modifiers such as score etc. See "Arguments section" for more information.

Usage

rba_uniprot_antigens_search(
  accession = NULL,
  antigen_sequence = NULL,
  antigen_id = NULL,
  ensembl_id = NULL,
  match_score = NULL,
  ...
)

Arguments

accession

UniProtKB primary or secondary accession(s). You can supply up to 100 accession numbers.

antigen_sequence

Protein sequence in the antigenic site.

antigen_id

Human Protein Atlas (HPA) antigen ID. You can supply up to 20 IDs.

ensembl_id

Ensembl Stable Transcript ID. You can supply up to 20 IDs.

match_score

(Numeric) Minimum alignment score for the antigen sequence and the target protein sequence.

...

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

Details

Note that this is a search function. Thus, you are not required to fill every argument; You may use whatever combinations of arguments you see fit for your query.

Value

A list Where each element correspond to a UniProt protein (search hit) and Antigenic features are organized under the "features" sub-list.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/antigen"

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 - Antigen": rba_uniprot_antigens()

Examples

rba_uniprot_antigens_search(antigen_id = "HPA001060")