Retrieve Smith-Waterman bit scores among proteins from the same species. STRING uses these sequence-similarity scores as a proxy for protein homology.
Arguments
- ids
Character or Numeric: Your protein ID(s). It is strongly recommended to supply STRING IDs. See
rba_string_map_idsfor more information.- species
Numeric: (optional) NCBI Taxonomy identifier; Human Taxonomy ID is 9606. (Recommended, but required if your input contains more than 10 unique IDs.)
- ...
rbioapi option(s). See
rba_options's arguments manual for more information on available options.
Value
A data frame containing pairwise bit scores and self-hits for the supplied proteins. Both orientations of a pair can be returned.
Details
To retrieve the best similarity hit for each input protein in other STRING
species, see
rba_string_homology_inter.
STRING imports the similarity matrix from the Similarity Matrix of Proteins (SIMAP) project.
Corresponding API Resources
"POST https://string-db.org/api/{output-format}/homology?identifiers= {your_identifiers}&{optional_parameters}"
References
Damian Szklarczyk, Katerina Nastou, Mikaela Koutrouli, Rebecca Kirsch, Farrokh Mehryary, Radja Hachilif, Dewei Hu, Matteo E Peluso, Qingyao Huang, Tao Fang, Nadezhda T Doncheva, Sampo Pyysalo, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2025: protein networks with directionality of regulation, Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D730–D737, https://doi.org/10.1093/nar/gkae1113
See also
rba_string_map_ids,
rba_string_homology_inter
Other "STRING":
rba_string_annotations(),
rba_string_enrichment(),
rba_string_enrichment_image(),
rba_string_enrichment_ppi(),
rba_string_functional_terms(),
rba_string_homology_inter(),
rba_string_interaction_partners(),
rba_string_interactions_network(),
rba_string_map_ids(),
rba_string_network_image(),
rba_string_version()
Examples
# \donttest{
rba_string_homology_intra(ids = c("CDK1", "CDK2"), species = 9606)
# }