Analysis

Predict translation initiation rate (OSTIR)

Predict the translation initiation rate at each start codon in a bacterial mRNA using OSTIR, the open-source continuation of the Salis lab RBS Calculator, with ViennaRNA free energies. Returns the predicted rate plus the full thermodynamic breakdown (16S rRNA:mRNA hybridization, mRNA unfolding, spacing, standby site, start-codon binding) for every start codon found. Rates are on an arbitrary scale — compare them as ratios, not as absolute expression levels. Runs ViennaRNA on a shared service and is therefore rate limited (see 429/503).

post/rbs_predict

Request

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

Request body

sequencestring required

mRNA sequence, raw or FASTA — the 5' UTR plus at least the start of the CDS. DNA (T) and RNA (U) are both accepted and scored identically. A, C, G, T/U only. Max 10,000 nt.

startnumber

Optional 1-based position; only consider start codons beginning at or after it.

endnumber

Optional 1-based position; only consider start codons beginning at or before it.

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.

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.