Files & formats

Fetch sequence by accession

Fetch a public DNA/protein record by accession from NCBI Nucleotide, NCBI Protein, UniProt, or Ensembl (e.g. NM_000546, NP_000537, P04637, ENSG00000141510) — the whole record, or with start/end just that region of it, which is how you take a few kb out of a chromosome instead of downloading the chromosome. Only the accession is sent upstream. Use sequence_search first if you only know a gene/organism name, not an accession, or genome_region if you know the gene's name but not its coordinates. For an Ensembl transcript ID this returns spliced cDNA; for a gene ID it returns the full genomic locus (introns included) — Ensembl's own default for each ID type.

post/sequence_fetch

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/sequence_fetch
  • Auth: none required

Request body

accessionstring required

GenBank/RefSeq accession (e.g. NM_000546), UniProtKB accession (e.g. P04637), or Ensembl stable ID (e.g. ENSG00000141510, ENST00000335137).

db'auto' | 'nucleotide' | 'protein' | 'uniprot' | 'ensembl'

Database to query; auto-detects from the accession format.

format'fasta' | 'genbank'

Output format (GenBank is only available for NCBI accessions — UniProt and Ensembl are FASTA-only).

startinteger

First base of the region to fetch, counted from 1 and included. Requires end. NCBI accessions only.

endinteger

Last base of the region, included. Always greater than or equal to start — use strand for the other orientation, not a swapped pair.

strand1 | -1

1 returns the region as written; -1 returns its reverse complement. Only meaningful with start/end.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.