Analysis

Design a non-repetitive promoter library spanning a strength range

Build a set of sigma-70 promoters that (a) share no more than a chosen length of sequence with each other, so the library does not recombine with itself once integrated, and (b) span a range of predicted transcription rates, picked as an evenly log-spaced ladder. Variants are constructed deterministically from an IUPAC template holding the -35 and -10 consensus; their strengths are then estimated by the Promoter Calculator model. Rungs with no variant near them are reported as gaps rather than filled with the nearest thing. PREDICTED, NOT MEASURED: strengths carry R^2 = 0.45-0.60 against independent in vivo data, so treat the ladder as a ranked set to screen, not as calibrated numbers.

post/promoter_library_design

Request

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

Request body

librarySizeinteger required

How many promoters the ladder should have (2 to 24). Required: every other argument has a defensible default, so this is the one statement of intent, and without it an empty call would build and score a library nobody asked for.

targetMinnumber

Weakest rung, in the model's arbitrary transcription-rate units. OMIT THIS and the range is taken from what the built variants actually score, which is usually right: the units have no absolute meaning, so a default would describe nothing. Set it only to match a promoter you measured yourself.

targetMaxnumber

Strongest rung, same units. Omit with targetMin to use the variants' own range.

lmaxinteger

Longest stretch any two promoters in the library may share, in bp (default 12). This is the property that stops the library recombining with itself.

templatestring

IUPAC template every variant must match. Defaults to a sigma-70 layout holding TTGACA and TATAAT with a 17 nt spacer and randomised flanks. Change it to target a different architecture — but a template that randomises the boxes will produce members that are not promoters.

candidatePoolinteger

How many variants to build and score before selecting the ladder. A larger pool fills more rungs and costs one longer scan, not more round trips.

gcMinnumber

Lowest GC% a variant may have.

gcMaxnumber

Highest GC% a variant may have.

excludestring[]

Motifs no variant may contain, both strands — the restriction sites you clone with. Literal ACGT only.

seedinteger

Seeds variant construction; same seed, same variants.

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.