Files & formats

Fetch a gene's region from a genome

Find a gene in an assembly by symbol or locus tag and return its sequence with however much flanking DNA you ask for — the step before designing a knockout, a C-terminal tag or an HDR donor, where you know the gene's name but not its coordinates. Give the assembly accession (GCF_000005845.2 for E. coli K-12 MG1655) and the gene (araC, or the locus tag b0064). upstream is upstream OF THE GENE: on a minus-strand gene that is the higher genomic coordinate, and the sequence comes back 5'→3' along the gene either way. Only an EXACT symbol or locus-tag match is used — NCBI's text search is fuzzy and ranks unrelated genes first, so a loose match is reported as a refusal naming what it found rather than answered with the wrong locus.

post/genome_region

Request

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

Request body

assemblystring required

Assembly accession, with its version — e.g. GCF_000005845.2. GCF_ (RefSeq) carries annotation more often than GCA_.

genestring required

Gene symbol or locus tag, matched exactly and case-insensitively (araC, b0064).

upstreaminteger

Bases to include before the gene's 5' end (its promoter side).

downstreaminteger

Bases to include after the gene's 3' end.

format'fasta' | 'genbank'

GenBank brings the annotation that falls inside the region; FASTA is sequence only.

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.