KASPspoon

KASPspoon converts classical quantitative trait loci (QTL) markers into Kompetitive Allele Specific PCR (KASP) assay primers to enable high-throughput single nucleotide polymorphism (SNP) genotyping and fine mapping of genomic regions associated with causal variants.

Key Features:

• In silico and in vitro PCR analysis: Performs in silico PCR by approximate-match searching of user-entered primer pairs against provided sequences and incorporates in vitro PCR results for comparative analysis.
• Marker conversion: Converts classical QTL markers into KASP assay primers for SNP genotyping.
• Amplimer identification and selection: Identifies amplimers adjacent to genes, SNPs, or simple sequence repeats (SSRs) and selects appropriate amplimers by comparing in silico and in vitro PCR results.
• Genomic mapping correlation: Correlates genetic and physical positions of loci to translate different experimental genetic data types into positional markers.
• Primer set genome coverage: Reports genome coverage provided by primer sets to support PCR-walking across genomic regions.
• Visualization and output: Produces human-readable output files and Circos configuration files to visualize results from both in silico and in vitro analyses.

Scientific Applications:

• KASP assay primer design: Produces KASP primers for high-throughput SNP genotyping assays.
• Fine mapping of QTLs: Enables narrowing of genomic intervals after QTL studies to locate regions containing causal variants.
• Gene discovery: Facilitates discovery by prioritizing amplimers near genes, SNPs, or SSRs for downstream analysis.
• Genetic and physical map integration: Supports correlation of genetic and physical maps for diverse experimental genetic datasets.
• Applications in genetics, breeding, and medicine: Provides SNP assay resources useful in genetics research, plant breeding, and personalized medicine.

Methodology:

Simulates PCR by performing approximate-match searches of user-entered primer pairs against supplied sequences; compares in silico PCR results with in vitro PCR results to select amplimers; correlates genetic and physical positions of loci and reports primer-set genome coverage; generates Circos configuration files and human-readable outputs.