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mims-harvard/tooluniverse

tooluniverse-sequence-retrieval

Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation.

All-time #7194 First seen Feb 4, 2026
8-week activity · all time api

Installation

$ npx skills add mims-harvard/tooluniverse --skill tooluniverse-sequence-retrieval
View on skills.sh ↗ GitHub repository ↗

Summary

  • Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation.
  • Quality hierarchy: RefSeq (NM_/NP_) > RefSeq predicted (XM_/XP_) > GenBank submissions.
  • Use for fetching specific sequences by accession, gene-symbol-to-sequence lookup, transcript-isoform retrieval, and curated-vs-raw-submission preference.

Also in this package

Other skills from mims-harvard/tooluniverse · top by installs.

npx skills add mims-harvard/tooluniverse
tooluniverse-literature-deep-research 643 tooluniverse-image-analysis 637 tooluniverse-clinical-guidelines 466 tooluniverse 458 tooluniverse-drug-research 452 tooluniverse-clinical-trial-design 440 tooluniverse-drug-drug-interaction 432 setup-tooluniverse 427 tooluniverse-disease-research 419 tooluniverse-protein-structure-retrieval 416

Browse all from mims-harvard/tooluniverse

More details

Agent compatibility

Declared targets from SKILL.md / docs. Unmarked agents are not listed — the skill may still install via the CLI.

Claude Code Not declared
Cursor Not declared
Codex Not declared
GitHub Copilot Not declared
Windsurf Not declared
Gemini CLI Not declared
Cline Not declared
OpenCode Not declared

Repository health

Stars 1.7K
License LICENSE
Default branch main
Open issues 9
Status Active

Package contents

Files included with this skill beyond the listing page.

  • skill md SKILL.md 5,901 B
  • docs SUMMARY.md 351 B

History

  1. First seen on skills.sh
  2. First recorded snapshot · 1,636 installs

SKILL.md

Biological 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
NCBIgetsequence ENA (if GenBank format) NCBI unavailable
enagetentry NCBIgetsequence ENA doesn't have RefSeq
NCBIsearchnucleotide Try broader keywords No results

Phase 3: Report Sequence Profile

Present as a Sequence Profile Report. Hide search process. Include:

  1. Search Summary: query, database, result count
  2. Primary Sequence: accession, type (RefSeq/GenBank), organism, strain, length, molecule, topology, curation level
  3. Sequence Preview: first lines of FASTA (truncated)
  4. Annotations Summary: CDS/tRNA/rRNA/regulatory feature counts (from GenBank format)
  5. Alternative Sequences: ranked by relevance and curation, with ENA compatibility
  6. Cross-Database References: RefSeq, GenBank, ENA/EMBL, BioProject, BioSample
  7. 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

  1. What is the highest-quality accession available?
  2. Are there alternative accessions in other databases?
  3. What is the annotation completeness?
  4. Is the sequence from the expected organism/strain?
  5. 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: NCBIsearchnucleotide (search), NCBIfetchaccessions (UID→accession), NCBIgetsequence (retrieve) ENA Tools (GenBank/EMBL only): enagetentry (metadata), enagetsequencefasta (FASTA), enagetentrysummary (summary)

Search Parameters Reference

NCBIsearchnucleotide: operation="search", organism (scientific name), gene (symbol), strain, keywords, seqtype (completegenome/mrna/refseq), limit

NCBIgetsequence: operation="fetch_sequence", accession, format (fasta/genbank)