tooluniverse-sequence-retrieval
Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles. Creates detailed reports with sequence metadata, cross-database references, and download options. Use when users need nucleotide sequences, protein sequences, genome data, or mention GenBank, RefSeq, EMBL accessions.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-sequence-retrieval --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Biological Sequence Retrieval Retrieve DNA, RNA, and protein sequences with proper disambiguation and cross-database handling. **IMPORTANT**: Always use English terms in tool calls (gene names, organism names, sequence descriptions), even if the user writes in another language. Only try original-language terms as a fallback if English returns no results. Respond in the user's language. ## Workflow Overview ``` Phase 0: Clarify (if needed) ↓ Phase 1: Disambiguate Gene/Organism ↓ Phase 2: Search & Retrieve (Internal) ↓ Phase 3: Report Sequence Profile ``` --- ## Phase 0: Clarification (When Needed) Ask the user ONLY if: - Gene name exists in multiple organisms (e.g., "BRCA1" → human or mouse?) - Sequence type unclear (mRNA, genomic, protein?) - Strain/isolate matters (e.g., E. coli → K-12, O157:H7, etc.) Skip clarification for: - Specific accession numbers (NC_*, NM_*, U*, etc.) - Clear organism + gene combinations - Complete genome requests with organism specified --- ## Phase 1: Gene/Organism Disambiguation ### 1.1 Resolve Identifiers ```python from tooluniverse import ToolUniverse tu = ToolUniverse() tu.load_tools() # Strategy depends on input type if user_provided_accession: #
- Workflow Overview
- Phase 0: Clarification (When Needed)
- Phase 1: Gene/Organism Disambiguation
- 1.1 Resolve Identifiers
- 1.2 Accession Type Decision Tree
- 1.3 Identity Resolution Checklist
- Phase 2: Data Retrieval (Internal)
- 2.1 Search for Sequences
- 2.2 Retrieve Sequence Data
- 2.3 ENA Alternative (for GenBank/EMBL accessions)
- Fallback Chains
- Phase 3: Report Sequence Profile
- Output Structure
- Curation Level Tiers
What does the tooluniverse-sequence-retrieval skill do?
Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles. Creates detailed reports with sequence metadata, cross-database references, and download options. Use when users need nucleotide sequences, protein sequences, genome data, or mention GenBank, RefSeq, EMBL accessions.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-sequence-retrieval --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.