Analysis

Design a ribosome binding site (OSTIR)

Design a 5' UTR / ribosome binding site for a given CDS. Generates a spread of Shine-Dalgarno cores and SD-to-start spacings, scores every one with OSTIR in the context of your own CDS (which matters — the rate depends on how the RBS interacts with that CDS's 5' folding), and returns them ranked. Supply targetExpression to rank by closeness to a target rate instead of by maximum strength, and supply your existing 5' UTR to get a measured baseline and fold-change for each candidate. Runs ViennaRNA on a shared service and is therefore rate limited (see 429/503).

post/rbs_design

Request

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

Request body

cdsstring required

Coding sequence, raw or FASTA, starting at its start codon. Only the 5' end affects the prediction, so the first ~90 nt is enough. A, C, G, T/U only. Max 10,000 nt.

currentUtrstring

Optional: your existing 5' UTR (everything upstream of the start codon). Scored as a baseline so each candidate gets a fold-change against it.

leaderstring

Optional 5' context upstream of the designed RBS — the transcribed leader from your promoter. Affects the standby-site term. Defaults to a 20 nt unstructured poly-A leader.

targetExpressionnumber

Optional target rate on OSTIR's arbitrary scale. Candidates are then ranked by closeness to it (log-ratio) rather than by maximum strength. Only meaningful against a number produced by this same tool.

antiShineDalgarnostring

Optional anti-Shine-Dalgarno sequence (the 16S rRNA 3' end) to model a non-E. coli host. Omit to use OSTIR's own E. coli default.

limitnumber

How many ranked candidates to return. 1-60.

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.