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Install in OpenClaw
/install bio-chat-qpcr-primer-designer
Description
为 RT-qPCR 设计引物和 TaqMan 探针，支持跨外显子、3' 端错配校验及同源映射硬核模式。
README (SKILL.md)
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: Automatically maps exon-exon junctions from a well-annotated ortholog (e.g., Human NM_) to a predicted target transcript (e.g., Vero XM_) to ensure gDNA-safe design even when annotations are missing.
- High-GC Template Optimization: Specialized algorithms for templates with >70% GC content (e.g., Pseudorabies virus), automatically adjusting primer length and Tm weight to ensure specificity.
- SYBR & TaqMan Support: Designs optimized primer pairs for SYBR Green and triplex/probe sets for TaqMan assays with precise Tm matching.
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 exon junction mapping.
- Automated Design: Execute
scripts/design_qpcr_assay.pywith specific parameters:--target: Target accession--homolog: Human ortholog for mapping--offtarget: Accession for 3' specificity check
- Validation: Review the top-scoring primer/probe sets based on Tm, GC, 3' quality, and secondary structure.
Technical Standards
- Tm Calculation: Nearest-Neighbor (NN) model.
- gDNA Defense: Primers must span or flank exon-exon junctions.
- 3' Quality: Strict control of 3' GC-clamp and mismatch prevention.
Designed by ZJU PhD @ Bio-chat Community
Usage Guidance
This skill appears coherent with its stated purpose. Before installing or running: 1) Review the Python script if you have concerns—it's included in the package and will make outbound HTTPS requests to NCBI (efetch) to retrieve sequences/annotations. 2) Running the script requires Python and the 'requests' package (requirements.txt present but no installer provided). 3) If you pass a local FASTA path, the script will read that file—don't point it at sensitive system files. 4) The sequence parsing and Tm calculations are simplified; validate any critical assay designs with your standard lab QC and established tools. 5) Because the source is unknown, consider running the script in a sandboxed environment or reviewing code before executing in production.
Capability Analysis
Type: OpenClaw Skill
Name: bio-chat-qpcr-primer-designer
Version: 1.0.3
The skill bundle provides a specialized tool for RT-qPCR primer and probe design, fetching biological sequence data from the official NCBI Entrez API (eutils.ncbi.nlm.nih.gov). The core logic in `scripts/design_qpcr_assay.py` implements standard bioinformatics algorithms for sequence analysis, such as Tm calculation and exon-junction mapping, with no evidence of data exfiltration, malicious command execution, or prompt-injection attacks.
Capability Assessment
Purpose & Capability
The name/description (RT-qPCR primer and TaqMan probe design, homology mapping, high-GC optimization) match the included script and examples. Required resources (NCBI efetch calls, optional local FASTA input) are appropriate for the stated functionality; there are no unrelated environment variables, binaries, or external services requested.
Instruction Scope
SKILL.md instructs the agent to fetch sequences by accession or read a provided FASTA and run scripts/design_qpcr_assay.py with arguments (target, homolog, offtarget). The script performs only those actions: HTTP GETs to NCBI eutils and optional local FASTA file reads. There are no instructions to access unrelated system files, other credentials, or to transmit data to unknown endpoints.
Install Mechanism
This is instruction-only (no install spec). A requirements.txt lists 'requests' but no automated installer is provided; the agent or user will need Python + requests to run the script. This is a minor usability inconsistency, not a security concern, but the script will perform network calls when executed.
Credentials
The skill requests no environment variables, credentials, or config paths. Network access is only to NCBI eutils (expected). The ability to read a user-supplied FASTA file is necessary for local sequence inputs; it does not read arbitrary system config by default.
Persistence & Privilege
The skill is not always-enabled and is user-invocable; it does not request persistent privileges or modify other skills. Autonomous invocation is allowed by default but is not combined with broad credential access or other red flags.
How to Use
- Make sure OpenClaw is installed (local or Docker)
- Run the install command in chat:
/install bio-chat-qpcr-primer-designer - After installation, invoke the skill by name or use
/bio-chat-qpcr-primer-designer - Provide required inputs per the skill's parameter spec and get structured output
Version History
v1.0.5
Version 1.0.5 of "bio-chat-qpcr-primer-designer" contains no changes from the previous version.
- No file changes or updates detected.
- All features and descriptions remain the same as in the previous release.
v1.0.4
No user-facing changes in this version.
- No file or documentation updates detected.
- All features and descriptions remain unchanged from the previous version.
v1.0.3
- Updated skill description to emphasize advanced features: cross-species homology mapping and high-GC virus template optimization.
- Rewrote documentation in English for broader accessibility and clarity.
- Added detailed workflow section explaining input formats, parameters, and usage scenarios.
- Highlighted key technical standards such as Nearest-Neighbor Tm calculation and strict gDNA defense.
- Removed older usage examples and simplified guidance for streamlined primer/probe design.
v1.0.2
- Removed 7 files, including documentation, examples, and main script files.
- Added requirements.txt for dependency management.
- No changes to SKILL.md content or feature set.
v1.0.1
RT-qPCR Primer Designer v1.0.1
- Added complete documentation and usage examples, including separate README and detailed SKILL description in both English and Chinese.
- Introduced new workflow and design rules for highly specific RT-qPCR primer and probe design, with support for exon-exon spanning, 3' mismatch checks, and cross-species homolog mapping.
- Included template scripts, guidelines, and reference examples for human and monkey GAPDH sequences.
- Provided hardcore mode for homology-mapping where exon annotation is absent, ensuring greater flexibility for non-model organisms.
v1.0.0
- Initial release of highly specific RT-qPCR primer design workflow.
- Supports mRNA detection with homolog discrimination and prevention of gDNA amplification.
- Implements alignment, exon-exon junction mapping, 3' mismatch specificity, and validation steps.
- Integrates automated primer and probe design script with NCBI sequence fetching.
- Includes detailed usage examples for both primer and probe design.
Metadata
Frequently Asked Questions
What is qpcr-primer-designer?
为 RT-qPCR 设计引物和 TaqMan 探针，支持跨外显子、3' 端错配校验及同源映射硬核模式。 It is an AI Agent Skill for Claude Code / OpenClaw, with 323 downloads so far.
How do I install qpcr-primer-designer?
Run "/install bio-chat-qpcr-primer-designer" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.
Is qpcr-primer-designer free?
Yes, qpcr-primer-designer is completely free, licensed under MIT-0. You can download, install and use it at no cost.
Which platforms does qpcr-primer-designer support?
qpcr-primer-designer is cross-platform and runs anywhere OpenClaw / Claude Code is available (cross-platform).
Who created qpcr-primer-designer?
It is built and maintained by zjuphD (@zjuphd); the current version is v1.0.3.
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