Enzymes & cloning

Construct auto-fix (domestication)

Iteratively substitutes synonymous codons to resolve unwanted restriction sites (domestication for Golden Gate), homopolymers, tandem repeats, predicted secondary structure, cryptic RBS/polyA motifs and hidden alternate-frame ORFs that construct_qc flags — without changing the encoded protein (verified). Does NOT touch premature stops or GC extremes; re-run construct_qc afterward to confirm. A native TypeScript alternative to a constraint-solver sidecar.

Batchable via POST /batch.

Chainable in workflows (passes its sequence field to the next step).

post/construct_autofix

Request

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

Request body

sequencestring required

Nucleotide sequence (raw or FASTA; IUPAC accepted).

organism'ecoli' | 'human' | 'yeast' | 'cho' | 'pichia' | 'insect' | 'arabidopsis' | 'zebrafish'

Codon-usage table to prefer among synonymous options.

frameStartinteger

1-based nucleotide where the reading frame begins.

avoidEnzymesstring[]

Enzyme names whose internal sites should be removed (e.g. ["BsaI","BsmBI"] for Golden Gate domestication).

gcWindowinteger
gcLownumber
gcHighnumber
homopolymerMininteger
crypticOrfMinAainteger

Minimum peptide length (aa) for a hidden alternate-frame ORF to be flagged.

maxPassesinteger

Repeat full passes until clean or no further progress.

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.