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Get Best Protein Similarity Hits Across Species

Source: R/stringdb.R
rba_string_homology_inter.Rd

Retrieve the highest Smith-Waterman bit-score hit between each input protein and proteins in every other STRING species. STRING uses these sequence-similarity scores as a proxy for protein homology.

Usage

rba_string_homology_inter(ids, species = NULL, species_b = NULL, ...)

Arguments

ids

Character or Numeric: Your protein ID(s). It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information.

species

Numeric: (optional) NCBI Taxonomy identifier of your input proteins; Human Taxonomy ID is 9606. (Recommended, but required if your input contains more than 10 unique IDs.)

species_b

Numeric: (optional) One or more NCBI Taxonomy identifiers used to restrict the search for closest homologs. The default is NULL, which searches all STRING species.

...

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

Value

A data frame containing each input protein and its closest homolog in every other STRING species, or in the species selected by species_b.

Details

To retrieve pairwise similarity scores among input proteins within one species, see rba_string_homology_intra.

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_best? 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

  • STRING API Documentation

  • Citations note on STRING website

See also

rba_string_map_ids, rba_string_homology_intra

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_image(), rba_string_enrichment_ppi(), rba_string_functional_terms(), rba_string_homology_intra(), rba_string_interaction_partners(), rba_string_interactions_network(), rba_string_map_ids(), rba_string_network_image(), rba_string_version()

Examples

# \donttest{
## Find the best hit in mouse and fruit fly for the human input protein
rba_string_homology_inter(ids = "CDK1",
    species = 9606,
    species_b = c(10090, 7227))
# }
# \donttest{
rba_string_homology_inter(ids = "ENSP00000269305", species = 9606)
# }