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
Your protein ID(s). It is strongly recommended to supply STRING IDs. See
rba_string_map_idsfor more information.- species
Numeric: 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. STRING returns only one half of the symmetric similarity matrix to reduce data transfer.
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, 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
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)
# }