Enzymes & cloning

Find a non-repetitive subset of existing parts

Given a toolbox of genetic parts, return the largest subset in which no two parts share more than a chosen length of sequence — on either strand. Parts that share a long stretch recombine into each other in a multi-part assembly and are the single largest cause of DNA synthesis failure, and neither shows up when the parts are checked one at a time. Reports every conflicting pair and why each dropped part was dropped. Deterministic: no model, no rate, no score. Use nonrepetitive_parts_design to build new parts instead of selecting from existing ones.

post/nonrepetitive_parts_find

Request

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

Request body

partsstring required

The toolbox as (multi-)FASTA — each record's header becomes the part's name. Max 4,000 parts, 5,000 bp each.

lmaxinteger

Longest stretch two parts may share, in bp (default 15). Two parts conflict when they share MORE than this. Below 8 bp every pair of sequences matches by chance.

bothStrandsboolean

Count a shared stretch even when one part carries it reverse-complemented. Recombination and synthesis both see both strands, so leaving this on is almost always right.

strategy'2apx' | 'greedy'

Which approximation picks the subset. Maximum independent set is NP-hard, so neither is guaranteed largest: '2apx' is the standard 2-approximation, 'greedy' repeatedly drops the most-conflicting part. Try both — they disagree on real toolboxes.

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.