Analysis

Search a sequence against GenBank (BLAST)

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.

post/blast_submit

Request

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

Request body

sequencestring 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.

databasestring

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).

hitlistSizeinteger

Most database sequences to report (1-100).

evaluenumber

Report only hits at or below this expect value. NCBI's default is 10.

typeMaterialboolean

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.

megablastboolean

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

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.