How do I install the Rtqpcr Primer Design skill?

Run npx skillmds@latest add dvcrn/rtqpcr-primer-design in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Rtqpcr Primer Design safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: executes scripts. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Rtqpcr Primer Design?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Rtqpcr Primer Design free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Rtqpcr Primer Design?

dvcrn (@dvcrn) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Rtqpcr Primer Design by dvcrn — Agent Skill

Name: Rtqpcr Primer Design
Rating: 4.2 (5 reviews)
Author: dvcrn

Rtqpcr Primer Design

Advanced RT-qPCR primer and probe design with specialized support for cross-species homology mapping (e.g., Human to Vero cells) and high-GC virus optimization. Use when needing to design high-specificity qPCR assays for: (1) Standard Human/Mouse/Monkey transcripts, (2) Predicted transcripts (XM_) lacking exon data via homology mapping, (3) High-GC viral templates (e.g., PRV), or (4) SYBR Green and TaqMan probe-based assays. Designed by ZJU PhD.

dvcrn Updated Sep 8, 2026 32 repo stars

File contents

RT-qPCR Primer Design (Bio-chat Series)

This skill provides a professional-grade workflow for designing high-specificity RT-qPCR primers and probes, optimized for complex biological samples.

Key Capabilities

Homology-based Junction Mapping: Uses multiple anchor points and sliding-window alignment to map exon-exon junctions from a well-annotated ortholog (e.g., Human NM_) to a predicted target transcript (e.g., Vero XM_). This ensures gDNA-safe design even when target annotations are missing.
High-GC Template Optimization: Implements the full SantaLucia (1998) Nearest-Neighbor thermodynamic model for precise Tm calculation, essential for templates with >70% GC content (e.g., Pseudorabies virus).
TaqMan & SYBR Green Support:
- TaqMan: Automatically designs probes with Tm 8-10°C higher than primers, following standard real-time PCR design rules (no 5' G, no poly-G runs).
- SYBR: Strict 3' quality control and secondary structure screening to minimize primer-dimers.
Off-target Defense: Supports an optional --offtarget transcript to check for 3' end mispriming, ensuring high specificity in mixed cDNA samples.

Workflow

Target Identification: Provide a NCBI Accession (NM_/XM_) or a local FASTA sequence.
Homology Mapping (Optional): For predicted monkey transcripts, provide a Human ortholog Accession to activate "Hardcore Mode" for junction mapping.
Automated Design: Execute scripts/design_qpcr_assay.py with specific parameters:
- --target: Target accession (e.g., NM_001256799)
- --homolog: Human ortholog for mapping (e.g., NM_001256799 for a monkey gene)
- --offtarget: Accession for 3' specificity check (e.g., a homologous gene in the same family)
Validation: Review the top-scoring sets based on Tm, GC, 3' quality, and gDNA safety.

Technical Standards

Tm Calculation: SantaLucia (1998) Nearest-Neighbor (NN) model with salt and terminal correction.
gDNA Defense: Primers are required to span exon-exon junctions by at least 5bp on each side for stability.
3' Quality: Strict GC-clamp control and mismatch prevention.

Designed by ZJU PhD @ Bio-chat Community

---name: rtqpcr-primer-designdescription: Advanced RT-qPCR primer and probe design with specialized support for cross-species homology mapping (e.g., Human to Vero cells) and high-GC virus optimization. Use when needing to design high-specificity qPCR assays for: (1) Standard Human/Mouse/Monkey transcripts, (2) Predicted transcripts (XM_) lacking exon data via homology mapping, (3) High-GC viral templates (e.g., PRV), or (4) SYBR Green and TaqMan probe-based assays. Designed by ZJU PhD.---# RT-qPCR Primer Design (Bio-chat Series)This skill provides a professional-grade workflow for designing high-specificity RT-qPCR primers and probes, optimized for complex biological samples.## Key Capabilities1. **Homology-based Junction Mapping**: Uses multiple anchor points and sliding-window alignment to map exon-exon junctions from a well-annotated ortholog (e.g., Human NM_) to a predicted target transcript (e.g., Vero XM_). This ensures gDNA-safe design even when target annotations are missing.2. **High-GC Template Optimization**: Implements the full SantaLucia (1998) Nearest-Neighbor thermodynamic model for precise Tm calculation, essential for templates with >70% GC content (e.g., Pseudorabies virus).3. **TaqMan & SYBR Green Support**: - **TaqMan**: Automatically designs probes with Tm 8-10°C higher than primers, following standard real-time PCR design rules (no 5' G, no poly-G runs). - **SYBR**: Strict 3' quality control and secondary structure screening to minimize primer-dimers.4. **Off-target Defense**: Supports an optional `--offtarget` transcript to check for 3' end mispriming, ensuring high specificity in mixed cDNA samples.## Workflow1. **Target Identification**: Provide a NCBI Accession (NM_/XM_) or a local FASTA sequence.2. **Homology Mapping (Optional)**: For predicted monkey transcripts, provide a Human ortholog Accession to activate "Hardcore Mode" for junction mapping.3. **Automated Design**: Execute `scripts/design_qpcr_assay.py` with specific parameters: - `--target`: Target accession (e.g., `NM_001256799`) - `--homolog`: Human ortholog for mapping (e.g., `NM_001256799` for a monkey gene) - `--offtarget`: Accession for 3' specificity check (e.g., a homologous gene in the same family)4. **Validation**: Review the top-scoring sets based on Tm, GC, 3' quality, and gDNA safety.## Technical Standards- **Tm Calculation**: SantaLucia (1998) Nearest-Neighbor (NN) model with salt and terminal correction.- **gDNA Defense**: Primers are required to span exon-exon junctions by at least 5bp on each side for stability.- **3' Quality**: Strict GC-clamp control and mismatch prevention.*Designed by ZJU PhD @ Bio-chat Community*

Frequently asked questions