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.
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
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)
# }