CRISPR

CRISPR on-target activity (Rule Set 3)

Score SpCas9 guides for on-target activity with Rule Set 3 (DeWeirdt et al., Nat Commun 2022) — the current successor to the Doench 2014 and CRISPRscan scores crispr_grna_design reports. Give a target sequence to find and score every NGG guide in it — on both strands unless searchReverseStrand says otherwise — or give 30-mer contexts directly. The tracrRNA MATTERS and is not cosmetic: Rule Set 3 models it as a feature, and the paper measures its accuracy dropping when the wrong one is specified. Returns a z-scored activity, which ranks guides against each other; it is not a percentage and not a probability of editing.

post/crispr_ontarget

Request

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

Request body

sequencestring

Target DNA to find NGG guides in. Give this OR contexts.

contextsstring[]

30-mer contexts to score directly: 4 nt upstream + 20 nt spacer + PAM + 3 nt downstream. Give this OR sequence.

searchReverseStrandboolean

Also scan the reverse strand for guides. Applies to sequence only; a 30-mer in contexts is already written on its own guide's strand.

tracr'Hsu2013' | 'Chen2013'

Which tracrRNA the guides will be paired with. Hsu2013 is the one in lentiCRISPRv2 and most published libraries; Chen2013 is the sgRNA(F+E) scaffold used by the Sanger/Yusa libraries. If you use the DeWeirdt (2020) tracrRNA, the paper reports Chen2013 as the better proxy — there is no DeWeirdt option in the model itself.

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.