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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

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

species

Numeric: 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: 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, Rebecca Kirsch, Mikaela Koutrouli, Katerina Nastou, Farrokh Mehryary, Radja Hachilif, Annika L Gable, Tao Fang, Nadezhda T Doncheva, Sampo Pyysalo, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D638–D646, https://doi.org/10.1093/nar/gkac1000

  • 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{
rba_string_homology_inter(ids = "p53",
    species = 9606,
    species_b = 7070)
# }
# \donttest{
rba_string_homology_inter(ids = "ENSP00000269305", species = 9606)
# }