Skip to contents

Using this function, you can retrieve the Smith-Waterman bit scores among proteins of the same species. Bit Scores serve as similarity scores between protein sequence; And, according to STRING documentations, as a proxy for protein homology.


rba_string_homology_intra(ids, species = NULL, ...)



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


Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606. (Recommended, but optional if your input is less than 100 IDs.)


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


A data frame with bit scores between your supplied proteins and their self-hit. To Reduce the transferred data, STRING returns only one half of the similarity matrix; This will not pose a problem because similarity matrix is symmetrical.


Note that this function will retrieve similarity scores of different proteins "within the same species". To Get a similarity scores of a given protein and it's closets homologous proteins in other species, see rba_string_homology_inter.
Similarity matrix is imported -by STRING- from: Similarity Matrix of Proteins (SIMAP)

Corresponding API Resources

"POST[output-format]/homology?identifiers= [your_identifiers]"


  • Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D605–D612,

  • STRING API Documentation

  • Citations note on STRING website


# \donttest{
rba_string_homology_intra(ids = c("CDK1", "CDK2"), species = 9606)
# }