Biological Sequence Retrieval
FreeEfficiently fetch and disambiguate biological sequences.
Free · Opens the source repo
What Biological Sequence Retrieval does
The Biological Sequence Retrieval skill allows users to retrieve DNA, RNA, and protein sequences from trusted databases like NCBI and ENA, ensuring high-quality and accurate results. It emphasizes a structured workflow to clarify queries, disambiguate gene and organism information, and effectively search and report sequences. This skill is particularly useful for researchers, bioinformaticians, and anyone involved in genomic studies who require reliable access to biological data.
The skill operates on a clear hierarchy of sequence quality, preferring RefSeq curated sequences over GenBank submissions. Users can fetch specific sequences by their accession numbers or perform lookups using gene symbols. The retrieval process is designed to be efficient, with built-in mechanisms to handle potential ambiguities in gene and organism identification. For example, if a gene exists in multiple organisms, the skill prompts for clarification to ensure accurate results.
In addition to fetching sequences, the skill provides a comprehensive Sequence Profile Report that summarizes the search results, including crucial details like accession numbers, sequence types, and annotations. This report format is designed to facilitate downstream analysis, making it easier for users to interpret and utilize the retrieved data in their research or applications.
Overall, this skill is an essential tool for anyone needing to access biological sequences with precision and clarity, streamlining the often complex process of genomic data retrieval and interpretation.
When to use it
Use this skill when you need to fetch specific DNA, RNA, or protein sequences from NCBI or ENA, especially when disambiguation is required.
When not to use it
This skill may not be suitable for users who require extensive data analysis or visualization, as it focuses solely on retrieval and reporting.
What you can build with it
Fetching Specific Sequences
Use the skill to retrieve a specific DNA or protein sequence by providing its accession number for quick access.
Disambiguating Gene Information
When working with genes present in multiple organisms, this skill helps clarify and disambiguate to ensure accurate data retrieval.
Generating Sequence Reports
After retrieving sequences, generate a comprehensive report that summarizes key details and annotations for further analysis.
How to install Biological Sequence Retrieval
View source1. Install with the skills CLI
npx skills add mims-harvard/tooluniverse/tooluniverse-sequence-retrieval --agent claude-code2. Or install it manually
Download the skill folder and drop it into ~/.claude/skills/ for all projects, or .claude/skills/ to scope it to one repo. Restart Claude Code so it picks up the new skill.
Anthropic's agentic coding CLI, and the reference implementation of Agent Skills. Drop a skill folder into ~/.claude/skills and Claude Code loads it automatically whenever a task matches the skill's description. Claude Code docs
Inside SKILL.md
Written by mims-harvardBiological Sequence Retrieval
Retrieve DNA, RNA, and protein sequences with proper disambiguation and cross-database handling.
IMPORTANT: Always use English terms in tool calls. Only try original-language terms as fallback. Respond in the user's language.
LOOK UP DON'T GUESS: Never assume accession numbers or sequence versions. Always retrieve and verify from NCBI or ENA.
Domain Reasoning
Sequence quality hierarchy: RefSeq (NM_/NP_ = curated) > RefSeq predicted (XM_/XP_) > GenBank (submitted). Prefer the MANE Select transcript for human canonical isoforms. Check version numbers -- annotations improve across versions.
Workflow
Phase 0: Clarify (if needed) → Phase 1: Disambiguate Gene/Organism → Phase 2: Search & Retrieve → Phase 3: Report
Phase 0: Clarification (When Needed)
Ask ONLY if: gene exists in multiple organisms, sequence type unclear, or strain matters. Skip for: specific accessions, clear organism+gene combos, complete genome requests with organism.
Phase 1: Gene/Organism Disambiguation
Accession Type Decision Tree
| Prefix | Type | Use With |
|---|---|---|
| NC_/NM_/NR_/NP_/XM_ | RefSeq | NCBI only |
| U*/M*/K*/X*/CP*/NZ_ | GenBank | NCBI or ENA |
| EMBL format | EMBL | ENA preferred |
CRITICAL: Never try ENA tools with RefSeq accessions -- they return 404.
Identity Checklist
- Organism confirmed (scientific name)
- Gene symbol/name identified
- Sequence type determined (genomic/mRNA/protein)
- Accession prefix identified for tool selection
Phase 2: Data Retrieval (Internal)
Retrieve silently. Do NOT narrate the search process.
# Search NCBI Nucleotide
result = tu.tools.NCBI_search_nucleotide(
operation="search", organism=organism, gene=gene,
strain=strain, keywords=keywords, seq_type=seq_type, limit=10
)
# Get accessions from UIDs
accessions = tu.tools.NCBI_fetch_accessions(operation="fetch_accession", uids=result["data"]["uids"])
# Retrieve sequence (FASTA or GenBank format)
sequence = tu.tools.NCBI_get_sequence(operation="fetch_sequence", accession=accession, format="fasta")
# ENA alternative (non-RefSeq accessions only)
entry = tu.tools.ena_get_entry(accession=accession)
fasta = tu.tools.ena_get_sequence_fasta(accession=accession)
Fallback Chains
| Primary | Fallback | Notes |
|---|---|---|
| NCBI_get_sequence | ENA (if GenBank format) | NCBI unavailable |
| ena_get_entry | NCBI_get_sequence | ENA doesn't have RefSeq |
| NCBI_search_nucleotide | Try broader keywords | No results |
Phase 3: Report Sequence Profile
Present as a Sequence Profile Report. Hide search process. Include:
- Search Summary: query, database, result count
- Primary Sequence: accession, type (RefSeq/GenBank), organism, strain, length, molecule, topology, curation level
- Sequence Preview: first lines of FASTA (truncated)
- Annotations Summary: CDS/tRNA/rRNA/regulatory feature counts (from GenBank format)
- Alternative Sequences: ranked by relevance and curation, with ENA compatibility
- Cross-Database References: RefSeq, GenBank, ENA/EMBL, BioProject, BioSample
- Download Options: FASTA (for BLAST/alignment), GenBank (for annotation)
Curation Level Tiers
| Tier | Prefix | Description |
|---|---|---|
| RefSeq Reference (best) | NC_, NM_, NP_ | NCBI-curated, gold standard |
| RefSeq Predicted | XM_, XP_, XR_ | Computationally predicted |
| GenBank Validated | Various | Submitted, some curation |
| GenBank Direct | Various | Direct submission |
| Third Party | TPA_ | Third-party annotation |
Reasoning Framework
Sequence quality: Prefer RefSeq over GenBank. Check version numbers. Sequences with "PREDICTED" in definition are not experimentally validated.
Accession guidance: RefSeq = NCBI-only. GenBank = mirrored in ENA/EMBL. Default to RefSeq mRNA (NM_) for human/model organisms; most complete genome assembly for microbial queries.
Cross-database reconciliation: Same sequence may have different accessions (e.g., GenBank U00096 = RefSeq NC_000913 for E. coli K-12). Always report both when available. Discrepancies between GenBank/RefSeq typically indicate RefSeq curation corrected submission errors.
Synthesis Questions
- What is the highest-quality accession available?
- Are there alternative accessions in other databases?
- What is the annotation completeness?
- Is the sequence from the expected organism/strain?
- What download format suits the user's downstream analysis?
Error Handling
| Error | Response |
|---|---|
| "No search criteria provided" | Add organism, gene, or keywords |
| "ENA 404 error" | Likely RefSeq -- use NCBI only |
| "No results found" | Broaden search, check spelling, try synonyms |
| "Sequence too large" | Note size, provide download link instead |
Tool Reference
NCBI Tools: NCBI_search_nucleotide (search), NCBI_fetch_accessions (UID→accession), NCBI_get_sequence (retrieve)
ENA Tools (GenBank/EMBL only): ena_get_entry (metadata), ena_get_sequence_fasta (FASTA), ena_get_entry_summary (summary)
Search Parameters Reference
NCBI_search_nucleotide: operation="search", organism (scientific name), gene (symbol), strain, keywords, seq_type (complete_genome/mrna/refseq), limit
NCBI_get_sequence: operation="fetch_sequence", accession, format (fasta/genbank)
Frequently asked questions about Biological Sequence Retrieval
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