Analysis

Design an RBS library spanning a range of translation rates

Build a ladder of ribosome binding sites whose predicted translation initiation rates are evenly spread, in log space, across a range you choose — the standard way to titrate one enzyme's level in a pathway without guessing. Scores every SD-core/spacing/spacer-composition combination with OSTIR in your own CDS context, then picks one variant per rung. Rungs it cannot fill are reported as GAPS rather than filled with the nearest available variant, so a library that does not really span the range says so. PREDICTED, NOT MEASURED: the ordering comes from a model with ρ ≈ 0.39 against measured expression, which is what makes it usable for ranking a library you will screen and unusable for hitting an absolute number.

post/rbs_library_design

Request

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

Request body

cdsstring required

The coding sequence, raw or FASTA, starting at its start codon. Only the 5' end affects the prediction, so the first ~90 nt is enough. Max 10,000 nt.

leaderstring

Sequence upstream of the RBS (the 5' end of the transcript). OSTIR needs some 5' context for its standby-site term; a 20 nt A-rich leader is assumed when none is given, which is an assumption and not a measurement.

targetMinnumber

Weakest rung, in OSTIR's arbitrary units. OMIT THIS and the range is taken from what the candidates actually reach in your CDS context, which is usually what you want: the units have no absolute meaning, so a number carried over from a paper or a default describes nothing. Set it only when you are matching a value you measured yourself in the same context.

targetMaxnumber

Strongest rung, in the same arbitrary units. Omit with targetMin to use the candidates' own range.

librarySizeinteger

How many variants the ladder should have (default 8).

antiShineDalgarnostring

Override the host's anti-Shine-Dalgarno sequence. Defaults to the E. coli one OSTIR is parameterised on.

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.