Enzymes & cloning

Find unwanted regulatory elements in a construct

Scan a multi-gene construct, on both strands, for the sequence that quietly breaks operons: promoter-like -35/-10 pairs (including ones pointing backwards, which make antisense RNA), Shine-Dalgarno sequences positioned in front of an internal start codon, terminator-shaped hairpins with a U-tract, out-of-frame start codons inside a declared CDS, and exact direct repeats. Reports what MATCHED and how far it sits from consensus — it does not score a match or claim it transcribes. For an estimated promoter strength use promoter_predict; for a translation rate use rbs_predict.

post/operon_scan

Request

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

Request body

sequencestring required

The construct, raw, FASTA or GenBank. Max 100,000 bp.

maxPromoterMismatchesinteger

Total mismatches allowed across both consensus boxes (default 1). 0 finds only perfect consensus, which real promoters rarely are; above 2 the hit rate on random DNA climbs fast.

cdsStartinteger

1-based start of a coding sequence. Given with cdsEnd, out-of-frame start codons inside it are reported — without them that check is skipped, because 'out of frame' has no meaning until a frame is declared.

cdsEndinteger

1-based end of that coding sequence.

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.