kasp_primer_design

Active

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
}

What this tool wraps· 0 endpoints

min confidence0.70 0.50

No endpoints wrapped at confidence ≥ 0.50.

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com.seqbench/workbench

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