kasp_primer_design
ActiveTool of com.seqbench/workbench
declared in 1.1.0
Design KASP/ARMS allele-specific genotyping primers for a SNP: two allele-specific forward primers differing only at the 3' terminal base (one per allele), each with the standard KASP universal tail (FAM for allele A, HEX for allele B), a deliberate internal ARMS secondary mismatch near the 3' end whose strength complements the natural allele mismatch (strong↔weak), and one common downstream reverse primer sized to a chosen amplicon range. Reuses the site's nearest-neighbor Tm engine.
Parameters schema
{
"type": "object",
"required": [
"target",
"snpPosition",
"alleleA",
"alleleB"
],
"properties": {
"target": {
"type": "string",
"description": "Nucleotide sequence (raw or FASTA; IUPAC accepted)."
},
"alleleA": {
"type": "string",
"description": "First allele (single base) — gets the FAM tail."
},
"alleleB": {
"type": "string",
"description": "Second allele (single base) — gets the HEX tail."
},
"maxAmplicon": {
"type": "integer",
"default": 150,
"description": "Maximum amplicon length for the common reverse primer."
},
"minAmplicon": {
"type": "integer",
"default": 60,
"description": "Minimum amplicon length for the common reverse primer."
},
"snpPosition": {
"type": "integer",
"description": "1-based position of the SNP on the forward strand."
},
"targetCoreTm": {
"type": "number",
"default": 56,
"description": "Target Tm (°C) for the allele-specific primer core (before the universal tail)."
},
"addSecondaryMismatch": {
"type": "boolean",
"default": true,
"description": "Engineer the internal ARMS destabilising mismatch near the 3' end."
}
},
"additionalProperties": false
}No endpoints wrapped at confidence ≥ 0.70.
Parent server
com.seqbench/workbench
1/7 registries