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Primer Design and Specificity

Designs and audits PCR and RT-qPCR primers with Primer3 and local off-target screening

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
14 files

What it does

Lets the agent design PCR and qPCR primer pairs from a supplied DNA sequence, check existing primer pairs, and screen candidate primers against reference sequences for likely off-target amplification. It calculates melting temperatures and secondary structure with the Primer3 library under stated salt and oligo conditions, and it keeps coordinates and settings in a traceable report. It also labels results as computational candidates, not experimentally validated assays.

Great for

  • Molecular biology researchers preparing a PCR or RT-qPCR assay who want a documented, reproducible design record
  • Students learning primer design rules and how Primer3 parameters affect results
  • Lab staff auditing primers already in use against a new reference genome or isoform set

Skip it if

  • Wet-lab decisions for diagnostics or clinical use without experimental validation, because the tools only compute in-silico results
  • Degenerate, bisulfite, probe, or modified-base assays, which the bundled ordinary-DNA model does not support
  • Guide-RNA design or expression normalization, which the skill explicitly excludes

Try asking

  • “Design a qPCR primer pair for exon 3 of this human gene FASTA, product size 90-180 bp, and report the coordinates”
  • “Check whether these existing forward and reverse primers are likely to amplify paralogs in my reference set”
  • “Assess the melting temperatures and hairpin risk of these tailed cloning primers at my reaction salt concentrations”
  • “Screen this primer panel for cross-pair products before I order it”
Step-by-step guide: how to use Primer Design and SpecificityInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 14 original files, the MIT licence and an attribution note.

    primer-design.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip primer-design.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip primer-design.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Record the accession with its version and a SHA-256 hash of the template so results can be reproduced later.
  • Supply explicit exclusion regions (BED file) and paralog or host sequences for the off-target screen, since a good Primer3 score alone does not show specificity.
  • Review the generated report and verify the returned sequence against the reference before ordering or running any wet-lab experiment.

What's inside

  • assets/assay-report-template.md
  • assets/qpcr-config.json
  • assets/requirements.txt
  • references/design-workflows.md
  • references/input-contract.md
  • references/sources.md
  • references/specificity.md
  • references/thermodynamics.md
  • scripts/_common.py
  • scripts/_specificity.py
  • scripts/check_thermodynamics.py
  • scripts/design_primers.py
  • scripts/screen_specificity.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.