167_batch_canonical_sequence_retrieval

batch lookup
sequence
fasta
uniparc

Given a batch list of UniProt accessions, retrieve the amino acid sequence for each in a single query, matching BioMart's classic bulk "peptide" attribute pull

Use at

https://sparql.uniprot.org/sparql/

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>

SELECT
  ?protein
  ?sequence
WHERE {
  GRAPH <http://sparql.uniprot.org/uniparc> {
    VALUES ?protein { uniprotkb:P04637 uniprotkb:P01308 uniprotkb:Q13613 }
    ?uniparc up:sequenceFor ?protein .
    ?uniparc rdf:value ?sequence .
  }
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v1("?protein"):::projected 
  v3("?sequence"):::projected 
  v2("?uniparc")
  bind0[/VALUES ?protein/]
  bind0-->v1
  bind00(["uniprotkb:P04637"])
  bind00 --> bind0
  bind01(["uniprotkb:P01308"])
  bind01 --> bind0
  bind02(["uniprotkb:Q13613"])
  bind02 --> bind0
  v2 --"up:sequenceFor"-->  v1
  v2 --"rdf:value"-->  v3