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Get Similarity Scores Hits of Proteins in a Species

Source: R/stringdb.R
rba_string_homology_intra.Rd

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.

Usage

rba_string_homology_intra(ids, species = 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; 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.

Value

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.

Details

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 https://string-db.org/api/{output-format}/homology?identifiers= {your_identifiers}"

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_inter

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_ppi(), 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)
# }