Get natural variants in UniProt by NIH-NCBI SNP database identifier
Retrieve natural variant annotations of a sequence using UniProt protein accession, dbSNP or HGVS expression.
rba_uniprot_variation( id, id_type, source_type = NA, consequence_type = NA, wild_type = NA, alternative_sequence = NA, location = NA, save_peff = FALSE, ... )
id |
An ID which can be either a UniProt primary or secondary accession, NIH-NCBI dbSNP ID or HGVS expression. NIH-NCBI dbSNP id or HGVS Expression. |
id_type |
The type of provided ID argument, one of: "uniprot", "dbsnp" or "hgvs" |
source_type |
Variation's source type. You can choose up to two of: "UniProt", "large scale study" and/or "mixed". |
consequence_type |
Variation's consequence type. You can choose up to two of: "missense", "stop gained" or "stop lost". |
wild_type |
Wild type amino acid. Accepted values are IUPAC single-letter amino acid (e.g. D for Aspartic acid) and "*" for stop codon. You can provide up to 20 values. |
alternative_sequence |
Alternative amino acid. Accepted values are IUPAC single-letter amino acid (e.g. D for Aspartic acid) and "*" for stop codon and "-" for deletion. You can provide up to 20 values. |
location |
A valid amino acid range (e.g. 10-25) within the sequence range where the variation occurs. You can provide up to 20 values. |
save_peff |
Logical or Character:
|
... |
rbioapi option(s). Refer to |
A list where each element is a list that corresponds to a UniProt protein entry.
"GET https://www.ebi.ac.uk/proteins/api/variation/dbsnp/dbid"
"GET https://www.ebi.ac.uk/proteins/api/variation/hgvs/hgvs"
"GET https://www.ebi.ac.uk/proteins/api/variation/accession"
Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin, The Proteins API: accessing key integrated protein and genome information, Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W539–W544, https://doi.org/10.1093/nar/gkx237
Other "UniProt - Variation":
rba_uniprot_variation_search()
rba_uniprot_variation(id = "rs121434451", id_type = "dbsnp") rba_uniprot_variation(id = "NC_000008.11:g.22119227C>T", id_type = "hgvs") rba_uniprot_variation(id = "O43593", id_type = "uniprot")
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