WheatOmics 2.0 · Analysis tool

CAPS / dCAPS / KASP

Design primers that discriminate two alleles of a SNP by restriction digestion (CAPS/dCAPS) or by allele-specific KASP genotyping. CAPS uses a natural site created or destroyed by the SNP; dCAPS introduces 1-3 mismatches in the primer to create the site (Neff et al. 2002); KASP designs two allele-specific primers plus one common primer.

3 input modes Restriction-digest assays Specificity check

Design type:

Allele 1 sequence (WT)

Allele 2 sequence (mutant, identical except the SNP)

BLAST DB name

Selected BLAST database Loading databases…

Chromosome

Region start

Region end

SNP pos

Allele 1 base

Allele 2 base

The chromosome list comes from the chosen BLAST database, so the names are always the ones it actually uses. The region is fetched with blastdbcmd; SNP pos must lie inside it, and the database's base there must be one of the two alleles.

VariantHub dataset

Chromosome

Position (bp)

REF/ALT are read from the VCF with bcftools and the flank is fetched from the dataset's reference BLAST DB. Enter the chromosome as the VCF spells it — Chr1A for the Chinese Spring datasets, chr1A for Kronos; it is translated to the DB's naming automatically.

Mismatch max

Top designs

Restriction enzymes (checked = used)

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Specificity check database (used when you click "Check specificity" on a design; select one database)

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Advanced options

Primer length (min,max)

Tm range (°C)

Product size (bp)

Flank for coord/VCF (bp)

Designs

Rank	Mode	Enzyme	Recognition	Designed primer	Mismatches	Cut pos	Tm F / R	Product (bp)	Actions

CAPS / dCAPS / KASP

Designs Download TSV

KASP designs Download TSV

Designs

KASP designs