gene-structure-mapper

What This Skill Does

The gene-structure-mapper is a specialized OpenClaw tool designed to translate complex genomic data into clear, publication-ready visual diagrams. By interfacing directly with the Ensembl REST API, this skill programmatically fetches exon-intron architecture for any given gene symbol or Ensembl ID. It allows researchers and bioinformaticians to overlay UniProt protein domain annotations directly onto the genomic map, providing a structural context for functional regions. Furthermore, the skill supports the visualization of specific mutation hotspots, making it an essential tool for correlating genetic variants with structural domains. The output is highly flexible, supporting PNG, SVG, and PDF formats to ensure compatibility with both digital presentations and high-resolution academic publishing standards.

Installation

To integrate this skill into your environment, use the OpenClaw management command: clawhub install openclaw/skills/skills/aipoch-ai/gene-structure-mapper Once installed, ensure your local Python environment has the necessary dependencies for matplotlib and requests as defined in the package documentation.

Use Cases

This skill is built for professionals working in genetics, molecular biology, and biotechnology. Common use cases include:

• Generating high-quality figures for research manuscripts showing gene organization.
• Annotating structural consequences of specific mutations by mapping codon positions to exon locations.
• Rapidly comparing isoforms or splice variants of a target gene.
• Visualizing the spatial distribution of protein domains (e.g., DNA-binding domains) relative to introns and exons.
• Educational presentations where clear, simplified gene maps are required to explain splicing mechanics.

Example Prompts

1. "Generate a gene structure diagram for BRCA1 in PDF format and include protein domain annotations."
2. "Create a PNG diagram for the TP53 gene and mark the codon 248 and 273 mutation hotspots."
3. "Show me the structure of KRAS and export it as an SVG file for my upcoming presentation."

Tips & Limitations

• Connectivity: Since the tool relies on the Ensembl REST API, an active internet connection is required for non-demo tasks. If you are offline, use the --demo flag to test the functionality with hardcoded TP53 data.
• Precision: Ensure that gene symbols are standard (e.g., HGNC symbols). If a symbol is ambiguous, providing an Ensembl ID (e.g., ENSG00000141510) will yield more reliable results.
• Customization: While the tool outputs clean, professional plots by default, the SVG format is recommended if you intend to perform further manual aesthetic refinements in software like Adobe Illustrator or Inkscape. Always verify the output path if you have specific file organization requirements, as the default uses the gene name as the file prefix.