CAPS/dCAPS Primer Design

CAPS / dCAPS Primer Design

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

Allele 1 sequence (WT)

Allele 2 sequence (mutant, identical except the SNP)

BLAST DB name

Region (chrom:start-end)

SNP position (bp)

Allele 1 base

Allele 2 base

Flanking sequence is fetched from the BLAST database (blastdbcmd). Chrom naming follows the DB convention, e.g. chr1A for Chinese_Spring2.1.

VariantHub dataset

Chromosome

Position (bp)

REF/ALT are read from the VCF with bcftools and flanks are fetched from the dataset's reference BLAST DB.

Mismatch max

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Restriction enzymes (checked = used)

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Specificity check databases (used when you click "Check specificity" on a design; checked = checked against)

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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 Primer Design

Designs Download TSV

Designs