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在 OpenClaw 中安装
/install bio-chat-qpcr-primer-designer
功能描述
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。
使用说明 (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
安全使用建议
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.
功能分析
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.
能力评估
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.
如何使用
- 确保已安装 OpenClaw（本地或 Docker 部署）
- 在对话框中输入安装命令：
/install bio-chat-qpcr-primer-designer - 安装完成后，直接呼叫该 Skill 的名称或使用
/bio-chat-qpcr-primer-designer触发 - 根据 Skill 的参数说明提供必要输入，即可获得结构化输出
版本历史
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.
元数据
常见问题
qpcr-primer-designer 是什么？
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。 它是一个面向 Claude Code / OpenClaw 的 AI Agent Skill 插件，目前累计下载 323 次。
如何安装 qpcr-primer-designer？
在 OpenClaw 或 Claude Code 对话框中运行命令「/install bio-chat-qpcr-primer-designer」即可一键安装，无需额外配置。
qpcr-primer-designer 是免费的吗？
是的，qpcr-primer-designer 完全免费，采用 MIT-0 许可证，可自由下载、安装和使用。
qpcr-primer-designer 支持哪些平台？
qpcr-primer-designer 跨平台运行，可在任意部署了 OpenClaw / Claude Code 的环境中使用（cross-platform）。
谁开发了 qpcr-primer-designer？
由 zjuphD（@zjuphd）开发并维护，当前版本 v1.0.3。
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