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Search UniProt protein sequence features by description

Source: R/uniprot_proteins.R
rba_uniprot_features_type.Rd

Search for terms in the descriptions of one specified UniProt sequence annotation (feature) type. The function returns protein entries with at least one feature of that type whose description matches a supplied term.

Usage

rba_uniprot_features_type(terms, type, categories = NULL, types = NULL, ...)

Arguments

terms

Character: Terms to find in feature descriptions. You can supply up to 20 terms.

type

Character: Sequence annotation (feature) type whose descriptions are searched. One of: "INIT_MET", "SIGNAL", "PROPEP", "TRANSIT", "CHAIN", "PEPTIDE", "TOPO_DOM", "TRANSMEM", "DOMAIN", "REPEAT", "ZN_FING", "DNA_BIND", "REGION", "COILED", "MOTIF", "COMPBIAS", "ACT_SITE", "BINDING", "SITE", "NON_STD", "MOD_RES", "LIPID", "CARBOHYD", "DISULFID", "CROSSLNK", "VAR_SEQ", "VARIANT", "MUTAGEN", "UNSURE", "CONFLICT", "NON_CONS", "NON_TER", "HELIX", "TURN", "STRAND", or "INTRAMEM".

categories

Character: (optional) Sequence annotation (feature) categories to include in each returned entry. Accepted values are: "MOLECULE_PROCESSING", "TOPOLOGY", "SEQUENCE_INFORMATION", "STRUCTURAL", "DOMAINS_AND_SITES", "PTM", "VARIANTS" and/or "MUTAGENESIS". You can supply up to 20 categories.

types

Character: (optional) Sequence annotation (feature) types to include in each returned entry. Accepted values are the same as for type. You can supply up to 20 types.

...

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

Value

A list named by UniProt accession. Each element contains the entry metadata, sequence, and the annotations selected by categories and types in its features element. Without those optional filters, all annotations of each matching entry are returned.

Details

The type and terms arguments determine which protein entries match the search. The optional categories and types arguments only select the annotations included in each returned entry; they do not change which entries match.

Corresponding API Resources

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

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

  • Proteins API Documentation

  • Citations note on UniProt website

See also

Other "UniProt - Features": rba_uniprot_features(), rba_uniprot_features_search()

Examples

# \donttest{
rba_uniprot_features_type(
    terms = "Alzheimer", type = "VARIANT", types = "VARIANT")
# }