Analysis

What can base-pair over the ribosome binding site

Find every stretch of a transcript that is reverse-complementary to the ribosome's footprint (-20 to +13 around the start codon), with the length and nearest-neighbour Tm of each duplex, and flag the ones that cover the Shine-Dalgarno core or the start codon. This is the mechanism every translational switch runs on — riboswitch, toehold switch, RNA thermometer, antisense repressor — and the first thing to look at when a switch does not switch or a construct is unexpectedly silent. Also reports where a sensor domain can be inserted without touching the site. Deterministic base-pairing, not a folding prediction: use rna_fold to ask whether a given stem actually wins at 37 °C. Reports no switching ratio — see this tool's notes for why.

post/rbs_occlusion

Request

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

Request body

sequencestring required

The transcript: the 5' UTR plus at least the start of the CDS. DNA or RNA. Max 20,000 nt.

startCodonAtinteger

1-based position of the start codon to anchor the footprint on. Omit to use the first ATG/GTG/TTG — pass it when the transcript has several, which is the usual case for a real 5' UTR.

minSteminteger

Shortest duplex to report, in bp (default 6). Below 4 bp every sequence pairs with everything; a stem that actually holds a site shut is usually 8 bp or more.

maxLoopinteger

Largest number of unpaired bases allowed between an arm and its target (default 100).

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