# SeqHub API The SeqHub API gives you programmatic access to protein search and annotation tools built on top of Tatta Bio's genomic language models. ## Endpoints ### Protein Context Search Search our database of 130,000+ microbial genomes for contigs containing proteins most similar (by embedding distance) to your query protein(s). A **contig** is a contiguous stretch of sequenced DNA encoding multiple proteins. Each result is the genomic neighborhood surrounding your match, along with functional annotations and taxonomic information. - **Single query**: [`POST /api/v1/protein-contexts/search`](/api/protein-context-search) — search with one protein sequence. - **Multi-query**: [`POST /api/v1/protein-contexts/search/multi-query`](/api/protein-context-search-multi-query) — search for contigs where all query proteins co-occur in the same genomic neighborhood. ### Protein Annotation Annotate a batch of protein sequences with biological function by finding their closest match in SwissProt (UniProt's curated database). Returns a functional description, accession ID, similarity score, percent identity, and query coverage for each input sequence. - **Annotate** — [`POST /api/v1/protein-annotations`](/api/protein-annotation) — annotate one or more protein sequences. ## Authentication All requests require a personal access token (PAT). Generate one from the **API Tokens** section of your [SeqHub profile](https://seqhub.org). Pass the token in the `Authorization` header: ``` Authorization: Bearer ``` Your token is shown once when you create it. It starts with `seqhub_` — copy it exactly as shown. ## Limits **Rate limits:** 1000 requests per month for protein search endpoints, and 1000 requests per month for the annotation endpoint. **Batch size:** The annotation endpoint accepts up to 128 sequences per request. If you need higher limits, let us know! Please reach out to us at [team@tatta.bio](mailto:team@tatta.bio). ## Versioning The SeqHub API is currently in beta. The API is subject to breaking changes while in beta.