---
title: "Search a sequence against GenBank (BLAST)"
method: POST
path: "/blast_submit"
tags: ["Analysis"]
---

# Search a sequence against GenBank (BLAST)

`POST /blast_submit`

## Request

- Base URL: `https://seqbench.com/api/v1`
- URL: `https://seqbench.com/api/v1/blast_submit`
- Auth: none required

Submit a sequence to NCBI BLAST and get a request id back immediately — poll it with blast_poll. The program is inferred from the sequence (nucleotide to blastn, protein to blastp) unless you name one, and a query whose type does not match the named program is refused rather than silently returning nothing. Databases: blastn: nt, refseq_rna (default nt); blastx: nr (default nr); blastp: nr, swissprot (default nr); tblastn: nt (default nt). typeMaterial: true limits nt to sequences from type material (Entrez sequence_from_type) — what a 16S or ITS read should be identified against, since every hit is then a named species. Up to 20,000 residues per sequence. A multi-FASTA of up to 96 records is ONE search with each record reported separately (blast_poll's `queries`), never one concatenated query. Searches typically take 20-60 seconds; NCBI asks that a single search is polled no more than once a minute.

## Request body

- object
  - `sequence` string, required: DNA or protein to search, raw or FASTA. Up to 20,000 residues; several FASTA records are searched as separate queries in one request.
  - `program` 'blastn' | 'blastp' | 'blastx' | 'tblastn': BLAST program. Omit to infer from the sequence: blastn for nucleotide, blastp for protein. blastx translates a nucleotide query and searches proteins; tblastn searches translated nucleotide databases with a protein query.
  - `database` string: Database to search. Omit for the program's default. blastn: nt, refseq_rna (default nt); blastx: nr (default nr); blastp: nr, swissprot (default nr); tblastn: nt (default nt).
  - `hitlistSize` integer: Most database sequences to report (1-100).
  - `evalue` number: Report only hits at or below this expect value. NCBI's default is 10.
  - `typeMaterial` boolean: Limit an nt search to sequences from type material — the strains species names are defined by. Use it to identify a 16S or ITS read: unfiltered nt ranks uncultured clones and misfiled isolates beside them.
  - `megablast` boolean: blastn only. Megablast (the default) finds near-identical sequences and is what identifies a clone; set false for a slower search that also finds diverged ones. Left unset, a query shorter than megablast's 28-base seed runs as plain blastn, since megablast cannot seed it at all.

## Response `200`

Tool ran successfully.

- SuccessResponse: Standard success envelope returned by every single-tool call.
  - `ok` unknown, required
  - `tool` string, required: The tool slug that ran.
  - `result` object, required: Tool-specific output object. Its shape depends on the tool — call `GET /{tool}` or see the docs for each tool's fields.
  - `gate` GateResult
    - `pass` boolean, required: True if and only if every hard check passed.
    - `checks` GateCheck[], required
      - `id` string, required
      - `label` string, required
      - `severity` 'hard' | 'soft', required
      - `pass` boolean, required
      - `message` string, required
      - `value` number
      - `threshold` string
    - `notChecked` string[], required: Honest list of what this gate does NOT verify.
  - `provenance` Provenance, required
    - `apiVersion` string, required
    - `tool` union, required: Tool slug, or an array of slugs (one per step) for a workflow.
      - string
      - string[]
    - `generatedAt` string, date-time, required: ISO 8601 timestamp of when the result was generated.

## Other responses

- `400`: Invalid argument or the tool could not run.
- `404`: Unknown tool.
- `429`: Rate limited (metered tools only). Body carries code `rate_limited` and retryable `true`; honor the Retry-After header.
- `503`: A metered tool is momentarily at capacity. The identical request should succeed after Retry-After; body carries code `upstream_unavailable`.

---

[API](https://skmtc.dev/seqbench/apis/seqbench-api.md) · [All operations](https://skmtc.dev/seqbench/apis/seqbench-api/llms.txt) · [OpenAPI document](https://skmtc.dev/seqbench/apis/seqbench-api/revisions/132575216865?raw)