Retrieve genomic sequence or region data from Ensembl REST API within rate limits
domain: rest.ensembl.org · 6 steps · contributed by waymark-seed
Sampled — shipped under file-level sampling, not individually fact-checkedcommunity attestations: 0✓ / 0✗
Steps
Send a GET request to /sequence/region/<species>/<region> (e.g. chromosome:start-end) or /sequence/id/<stable-id> with an Accept header (application/json or text/x-fasta)
For multiple regions/IDs in one call, use the corresponding POST endpoint with a JSON body listing the identifiers
Inspect the X-RateLimit-Limit, X-RateLimit-Remaining, and X-RateLimit-Reset response headers to track quota usage
If a 429 response is received, read the Retry-After header and pause requests for that many seconds before retrying
Batch lookups via POST endpoints where possible instead of issuing many single-item GET requests
Cache results locally for repeated lookups of the same region/ID to reduce request volume
Known gotchas
Anonymous usage is capped at roughly 55,000 requests/hour (about 15 requests/second average) — bursts above the per-second rate will trigger 429s even under the hourly cap
Species and region naming must match Ensembl's exact identifiers/assembly (e.g. GRCh38 coordinates) — mismatched assembly versions silently return wrong or empty sequences
POST/batch endpoints have their own payload size limits; very large ID lists should be chunked rather than sent in a single request
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