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Data & Repro
TO
tooluniverse-sequence-retrieval
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tooluniverse-sequence-retrieval
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- 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.
- if user_provided_accession: # Direct retrieval based on accession type accession = user_provided_accession elif user_provided_gene_and_organism: # Search NCBI Nucleotide result = tu.tools.NCBI_search_nucleotide( operation="search", organism=organism, gene=gene, limit=10 ).
Source Doc
Excerpt From SKILL.md
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
1.1 Resolve Identifiers
from tooluniverse import ToolUniverse
tu = ToolUniverse()
tu.load_tools()
## 1.2 Accession Type Decision Tree
**CRITICAL**: Accession prefix determines which tools to use.
| Prefix | Type | Use With |
|--------|------|----------|
| NC_* | RefSeq chromosome | NCBI only |
| NM_* | RefSeq mRNA | NCBI only |
| NR_* | RefSeq ncRNA | NCBI only |
| NP_* | RefSeq protein | NCBI only |
| XM_* | RefSeq predicted mRNA | NCBI only |
| U*, M*, K*, X* | GenBank | NCBI or ENA |
| CP*, NZ_* | GenBank genome | NCBI or ENA |
| EMBL format | EMBL | ENA preferred |
Use cases
- Use when users need nucleotide sequences, protein sequences, genome data, or mention GenBank, RefSeq, EMBL accessions.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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