CRISPR

Design an extra-long sgRNA array

Build a multiplexed CRISPR array that expresses many sgRNAs from one cassette and shares no long stretch with itself. Twenty sgRNAs built the obvious way carry twenty copies of the same Cas9 scaffold, promoter and terminator — a construct that recombines in the cell and that synthesis vendors refuse — so this draws each transcription unit's parts from the measured non-repetitive collection of Reis et al. (2019), selecting ACROSS promoters, handles and spacers at once rather than within each type, then re-measures the assembled molecule for repeats the junctions created. Returns the sequence, an annotated GenBank file and the pool usage. Takes guides; it does not choose or score them — use crispr_grna_design and crispr_offtarget_check for that.

post/elsa_design

Request

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

Request body

guidesstring[] required

The 20 nt protospacers, in array order, WITHOUT their PAM. Strings, or {name, sequence} objects to label each unit. Max 27 — the size of the handle collection.

lmaxinteger

Longest stretch any two parts in the array may share, in bp (default 12). Lower is more stable and leaves fewer parts to choose from: the handle pool offers 12 at lmax 12, 18 at 15 and 24 at 20. Run elsa_capacity first.

insulateboolean

Place a neutral spacer between transcription units. Turning it off frees the spacer pool from the selection, which can let a longer array fit at a low lmax.

namestring

LOCUS name for the GenBank output.

includeGenbankboolean

Return the annotated GenBank file.

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.