Enzymes & cloning

Repeat instability (what the construct can delete)

Find the exact direct repeats in a construct that make it deletable, and build the molecule each pair would collapse to. Two copies of the same terminator or promoter in a multi-gene assembly let the DNA between them recombine out — silently, so the clone grows and the map looks right until it is sequenced. Returns each repeat pair's coordinates plus the resulting sequence(s), ordered by repeat length and spacer, the two factors that govern how readily a pair recombines. Reports no deletion RATE: none is derivable from sequence alone. Feed a deletion product to diagnostic_digest to screen for it.

Batchable via POST /batch.

post/repeat_instability

Request

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

Request body

sequencestring required

The construct, raw or FASTA. Max 500,000 bp.

circularboolean

Treat as a plasmid. A circular construct is searched across its own arbitrary start, so a repeat straddling position 1 is not missed, and each pair reports BOTH circles the recombination makes.

minRepeatLengthinteger

Shortest repeat to report, in bp (default 20). Below about 20 bp homologous recombination has little to work with and chance matches multiply.

maxPairsinteger

Cap on reported pairs, most recombinogenic first. The pre-cap count is always reported as pairsFound.

includeSequencesboolean

Return the full product sequences. Turn off for a coordinates-only summary over a large construct.

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.