CRISPR

Prime Editing Studio (pegRNA)

Design SpCas9 prime-editing pegRNAs for a substitution, insertion, deletion, or small replacement: for each usable NGG PAM it builds the spacer, a primer-binding-site (PBS) length sweep targeting a ~30 C melting temperature, the reverse-transcriptase template (RTT) that encodes the edit, and the full 3' extension, plus PE3 nicking-sgRNA suggestions 40-90 bp away on the opposite strand. Designs where the edit destroys the pegRNA's own PAM (preventing re-nicking of the edited allele) are ranked first. Coordinates: every pegRNA coordinate (protospacer span, nick position, editStart/editEnd) is 1-based inclusive in the submitted PRE-EDIT target's frame — the protospacer+PAM search runs on the unedited sequence, because Cas9 has to bind the allele you actually have. The one exception is edit-dependent PE3b nicking guides, which exist only once the edit is installed; each nickingGuides entry therefore carries a coordinateFrame field of "target" or "editedSequence" naming the frame its own start/end/nickToNickDistance are measured in, and for a length-changing edit the two frames differ downstream of the edit. Off-target activity is not evaluated (no in-browser reference genome).

post/prime_editing_design

Request

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

Request body

targetstring required

Forward-strand target DNA (raw or FASTA), with flanking sequence around the intended edit.

editStartinteger required

1-based inclusive start of the region being changed.

editEndinteger required

1-based inclusive end of the region being changed. For a pure insertion, set editEnd = editStart - 1.

insertedSeqstring

Replacement bases (forward strand). Empty string means a deletion.

rttHomologyinteger

Homology length (nt) 3' of the edit that the RTT should include (typically 10-16).

pbsLengthinteger

Optional preferred PBS length to highlight; a full 8-17 nt sweep is always returned.

frameStartinteger

Optional 1-based CDS reading-frame start, used only to annotate whether a PAM-blocking mutation would be silent.

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.