tooluniverse-sequence-retrieval
π―Skillfrom mims-harvard/tooluniverse
|Retrieves biological sequences from NCBI and ENA with precise gene disambiguation, accession handling, and comprehensive sequence metadata
Overview
A Claude Code skill that retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA databases with gene disambiguation, accession type handling, and comprehensive sequence profiles. It provides a structured workflow from clarification through disambiguation, retrieval, and detailed reporting with metadata and cross-database references.
Key Features
- Multi-Database Retrieval - Searches and retrieves sequences from both NCBI and ENA, with automatic routing based on accession prefix (NC_, NM_, NP_* for NCBI; EMBL format for ENA)
- Gene Disambiguation - Resolves ambiguous gene names across organisms and sequence types, asking for clarification only when genuinely needed
- Accession Type Decision Tree - Comprehensive mapping of accession prefixes (RefSeq, GenBank, EMBL) to the correct retrieval tools and databases
- Phased Workflow - Four-phase process: clarification when needed, gene/organism disambiguation, silent data retrieval, and detailed sequence profile reporting
- ToolUniverse Integration - Uses the ToolUniverse Python library for NCBI search, accession fetching, and sequence retrieval operations
Who is this for?
This skill is designed for bioinformaticians, molecular biologists, and researchers who need to retrieve and analyze biological sequences during their coding or analysis sessions. It is particularly valuable for those working with multiple sequence databases who want automated accession type routing and gene disambiguation without manually navigating database interfaces.
Same repository
mims-harvard/tooluniverse(70 items)
Installation
npx vibeindex add mims-harvard/tooluniverse --skill tooluniverse-sequence-retrievalnpx skills add mims-harvard/tooluniverse --skill tooluniverse-sequence-retrieval~/.claude/skills/tooluniverse-sequence-retrieval/SKILL.mdSKILL.md
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