prime_editing_design
ActiveTool of com.seqbench/workbench
declared in 1.1.0
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. Off-target activity is not evaluated (no in-browser reference genome).
Parameters schema
{
"type": "object",
"required": [
"target",
"editStart",
"editEnd"
],
"properties": {
"target": {
"type": "string",
"description": "Forward-strand target DNA (raw or FASTA), with flanking sequence around the intended edit."
},
"editEnd": {
"type": "integer",
"description": "1-based inclusive end of the region being changed. For a pure insertion, set editEnd = editStart - 1."
},
"editStart": {
"type": "integer",
"description": "1-based inclusive start of the region being changed."
},
"pbsLength": {
"type": "integer",
"description": "Optional preferred PBS length to highlight; a full 8-17 nt sweep is always returned."
},
"frameStart": {
"type": "integer",
"description": "Optional 1-based CDS reading-frame start, used only to annotate whether a PAM-blocking mutation would be silent."
},
"insertedSeq": {
"type": "string",
"default": "",
"description": "Replacement bases (forward strand). Empty string means a deletion."
},
"rttHomology": {
"type": "integer",
"default": 13,
"description": "Homology length (nt) 3' of the edit that the RTT should include (typically 10-16)."
}
},
"additionalProperties": false
}No endpoints wrapped at confidence ≥ 0.50.
Parent server
com.seqbench/workbench
1/7 registries