primer-design
Installation
SKILL.md
Primer design and specificity
Produce candidate oligos in 5-prime-to-3-prime orientation, with the exact template, chemistry, intended products, and search scope behind each conclusion. Calculate sequence-dependent quantities with the supplied tools. A familiar gene name, good Primer3 penalty, or a single BLAST alignment cannot establish primer specificity.
Choose the workflow
| Request | Start here |
|---|---|
| New genomic PCR or RT-qPCR pair | Define the assay and reference; design; assess thermodynamics; screen products. |
| Check an existing pair | Prepare pair TSV; assess both full oligos and annealing cores; screen with explicit intended coordinates. |
| Exon junction, transcript isoform, allele discrimination | Read design-workflows.md; supply sequence annotation before imposing constraints. |
| Cloning/adaptor-tailed primers | Design annealing cores, append declared 5-prime tails, reassess full oligos, reconstruct the final product. |
| Multiplex panel | Enable --multiplex in both thermodynamics and specificity tools to assess oligo interactions and cross-pair products. |
| Degenerate, bisulfite, probe, or modified-base assay | Use the specialized workflow in design-workflows.md; the bundled ordinary-DNA model is insufficient. |