Primers & oligos

KASP / ARMS Allele-Specific Primers

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 that primer's own natural allele mismatch (strong↔weak), and one common downstream reverse primer sized to a chosen amplicon range. Because a forward primer reads the antisense strand, each primer's 3' base sits opposite the complement of the other allele, so the two primers get different mismatch classes and are reported separately (graded from the measured PCR yields in Kwok et al. 1990). Reuses the site's nearest-neighbor Tm engine.

post/kasp_primer_design

Request

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

Request body

targetstring required

Nucleotide sequence (raw or FASTA; IUPAC accepted).

snpPositioninteger required

1-based position of the SNP on the forward strand. Must be 18 or greater: the allele-specific primers end on the SNP, so they need at least 17 bp of upstream template to build a core from.

alleleAstring required

First allele (single base) — gets the FAM tail.

alleleBstring required

Second allele (single base) — gets the HEX tail.

targetCoreTmnumber

Target Tm (°C) for the allele-specific primer core (before the universal tail).

minAmpliconinteger

Minimum amplicon length for the common reverse primer.

maxAmpliconinteger

Maximum amplicon length for the common reverse primer.

addSecondaryMismatchboolean

Engineer the internal ARMS destabilizing mismatch near the 3' end.

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.