CRISPR

HDR donor designer

Build an HDR donor (homology arms flanking an edit) from a target sequence and either an explicit edit window (editStart/editEnd) or a guide's cut site (guideStart/guideEnd/guideStrand/nuclease — SpCas9-family only; Cas12a's staggered cut needs an explicit editStart/editEnd). Also designs genotyping primers spanning the edit site on the original sequence (a real size-shift or sequencing target to confirm the edit), reusing the same primer-design engine as primer_design.

post/crispr_hdr_donor

Request

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

Request body

targetSequencestring required

Nucleotide sequence (raw or FASTA; IUPAC accepted).

editStartinteger

1-based start of the region being replaced. Omit to derive from guideStart/guideEnd/guideStrand instead.

editEndinteger

1-based inclusive end of the region being replaced; editEnd = editStart-1 denotes a pure insertion with nothing removed. Omit to derive from the guide's cut site.

guideStartinteger

1-based forward-strand start of the guide's protospacer (alternative to editStart/editEnd, for an insertion exactly at the cut site).

guideEndinteger

1-based forward-strand end of the guide's protospacer.

guideStrand'+' | '-'

Strand the guide's protospacer is on.

nuclease'spcas9' | 'spcas9ng' | 'sacas9' | 'cas12a'

Needed only when deriving the cut site from guideStart/guideEnd/guideStrand.

replacementstring required

Sequence to insert/substitute ("" for a pure deletion).

armLengthinteger

Homology arm length (bp) on each side. Use ~30–60 for an ssODN donor, ~500–1000 for a dsDNA donor plasmid.

designGenotypingPrimersboolean

Also design a primer pair (on the original targetSequence) whose product spans the edit site.

blockPamboolean

When a SpCas9-family guide is supplied and the edit does not already disrupt its PAM, fold a PAM-blocking mutation (silent when a CDS frame is given) into the donor so the edited allele can't be re-cut.

frameStartinteger

Optional 1-based CDS reading-frame start; makes the PAM-blocking mutation synonymous where possible.

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.