Agent skill

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.

View SKILL.md on GitHub Repository
Stars 2,009
Forks 275

Install this agent skill to your Project

npx add-skill https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tooluniverse-sequence-retrieval

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 (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:
    # 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
    )

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

1.3 Identity Resolution Checklist

  • Organism confirmed (scientific name)
  • Gene symbol/name identified
  • Sequence type determined (genomic/mRNA/protein)
  • Strain specified (if relevant)
  • Accession prefix identified → tool selection

Phase 2: Data Retrieval (Internal)

Retrieve silently. Do NOT narrate the search process.

2.1 Search for Sequences

python
# Search NCBI Nucleotide
result = tu.tools.NCBI_search_nucleotide(
    operation="search",
    organism=organism,
    gene=gene,
    strain=strain,  # Optional
    keywords=keywords,  # Optional
    seq_type=seq_type,  # complete_genome, mrna, refseq
    limit=10
)

# Get accession numbers from UIDs
accessions = tu.tools.NCBI_fetch_accessions(
    operation="fetch_accession",
    uids=result["data"]["uids"]
)

2.2 Retrieve Sequence Data

python
# Get sequence in desired format
sequence = tu.tools.NCBI_get_sequence(
    operation="fetch_sequence",
    accession=accession,
    format="fasta"  # or "genbank"
)

# GenBank format for annotations
annotations = tu.tools.NCBI_get_sequence(
    operation="fetch_sequence",
    accession=accession,
    format="genbank"
)

2.3 ENA Alternative (for GenBank/EMBL accessions)

python
# Only for non-RefSeq accessions!
if not accession.startswith(("NC_", "NM_", "NR_", "NP_", "XM_", "XR_")):
    # ENA entry info
    entry = tu.tools.ena_get_entry(accession=accession)
    
    # ENA FASTA
    fasta = tu.tools.ena_get_sequence_fasta(accession=accession)
    
    # ENA summary
    summary = tu.tools.ena_get_entry_summary(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

Critical Rule: Never try ENA tools with RefSeq accessions (NC_, NM_, etc.) - they will return 404 errors.

Phase 3: Report Sequence Profile

Output Structure

Present as a Sequence Profile Report. Hide search process.

markdown
# Sequence Profile: [Gene/Organism]

**Search Summary**
- Query: [gene] in [organism]
- Database: NCBI Nucleotide
- Results: [N] sequences found

---

## Primary Sequence

### [Accession]: [Definition/Title]

| Attribute | Value |
|-----------|-------|
| **Accession** | [accession] |
| **Type** | RefSeq / GenBank |
| **Organism** | [scientific name] |
| **Strain** | [strain if applicable] |
| **Length** | [X,XXX bp / aa] |
| **Molecule** | DNA / mRNA / Protein |
| **Topology** | Linear / Circular |

**Curation Level**: ●●● RefSeq (curated) / ●●○ GenBank (submitted) / ●○○ Third-party

### Sequence Statistics
| Statistic | Value |
|-----------|-------|
| **Length** | [X,XXX] bp |
| **GC Content** | [XX.X]% |
| **Genes** | [N] (if genome) |
| **CDS** | [N] (if annotated) |

### Sequence Preview
```fasta
>[accession] [definition]
ATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG
ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA
... [truncated, full sequence in download]

Annotations Summary (from GenBank format)

Feature Count Examples
CDS [N] [gene names]
tRNA [N] -
rRNA [N] 16S, 23S
Regulatory [N] promoters

Alternative Sequences

Ranked by relevance and curation level:

Accession Type Length Description ENA Compatible
NC_000913.3 RefSeq 4.6 Mb E. coli K-12 reference ✗
U00096.3 GenBank 4.6 Mb E. coli K-12 ✓
CP001509.3 GenBank 4.6 Mb E. coli DH10B ✓

Cross-Database References

Database Accession Link
RefSeq [NC_*] [NCBI link]
GenBank [U*] [NCBI link]
ENA/EMBL [same as GenBank] [ENA link]
BioProject [PRJNA*] [link]
BioSample [SAMN*] [link]

Download Options

Formats Available

Format Description Use Case
FASTA Sequence only BLAST, alignment
GenBank Sequence + annotations Gene analysis
GFF3 Annotations only Genome browsers

Direct Commands

python
# FASTA format
tu.tools.NCBI_get_sequence(
    operation="fetch_sequence",
    accession="[accession]",
    format="fasta"
)

# GenBank format (with annotations)
tu.tools.NCBI_get_sequence(
    operation="fetch_sequence",
    accession="[accession]",
    format="genbank"
)

Related Sequences

Other Strains/Isolates

Accession Strain Similarity Notes
[acc1] [strain1] 99.9% [notes]
[acc2] [strain2] 99.5% [notes]

Protein Products (if applicable)

Protein Accession Product Name Length
[NP_*] [protein name] [X] aa

Retrieved: [date] Database: NCBI Nucleotide


---

## Curation Level Tiers

| Tier | Symbol | Accession Prefix | Description |
|------|--------|------------------|-------------|
| RefSeq Reference | ●●●● | 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 |

Include in report:
```markdown
**Curation Level**: ●●●● RefSeq Reference
- Curated by NCBI RefSeq project
- Regular updates and validation
- Recommended for reference use

Completeness Checklist

Every sequence report MUST include:

Per Sequence (Required)

  • Accession number
  • Organism (scientific name)
  • Sequence type (DNA/RNA/protein)
  • Length
  • Curation level
  • Database source

Search Summary (Required)

  • Query parameters
  • Number of results
  • Ranking rationale

Include Even If Limited

  • Alternative sequences (or "Only one sequence found")
  • Cross-database references (or "No cross-references available")
  • Download instructions

Common Use Cases

Reference Genome

User: "Get E. coli K-12 complete genome"

python
result = tu.tools.NCBI_search_nucleotide(
    operation="search",
    organism="Escherichia coli",
    strain="K-12",
    seq_type="complete_genome",
    limit=3
)
# Return NC_000913.3 (RefSeq reference)

Gene Sequence

User: "Find human BRCA1 mRNA"

python
result = tu.tools.NCBI_search_nucleotide(
    operation="search",
    organism="Homo sapiens",
    gene="BRCA1",
    seq_type="mrna",
    limit=10
)

Specific Accession

User: "Get sequence for NC_045512.2" → Direct retrieval with full metadata

Strain Comparison

User: "Compare E. coli K-12 and O157:H7 genomes" → Search both strains, provide comparison table

Error Handling

Error Response
"No search criteria provided" Add organism, gene, or keywords
"ENA 404 error" Accession is likely RefSeq → use NCBI only
"No results found" Broaden search, check spelling, try synonyms
"Sequence too large" Note size, provide download link instead of preview
"API rate limit" Tools auto-retry; if persistent, wait briefly

Tool Reference

NCBI Tools (All Accessions)

Tool Purpose
NCBI_search_nucleotide Search by gene/organism
NCBI_fetch_accessions Convert UIDs to accessions
NCBI_get_sequence Retrieve sequence data

ENA Tools (GenBank/EMBL Only)

Tool Purpose
ena_get_entry Entry metadata
ena_get_sequence_fasta FASTA sequence
ena_get_entry_summary Summary info

Search Parameters Reference

NCBI_search_nucleotide

Parameter Description Example
operation Always "search" "search"
organism Scientific name "Homo sapiens"
gene Gene symbol "BRCA1"
strain Specific strain "K-12"
keywords Free text "complete genome"
seq_type Sequence type "complete_genome", "mrna", "refseq"
limit Max results 10

NCBI_get_sequence

Parameter Description Example
operation Always "fetch_sequence" "fetch_sequence"
accession Accession number "NC_000913.3"
format Output format "fasta", "genbank"

Recommended Agent Skills

Expand your agent's capabilities with these related and highly-rated skills.

FreedomIntelligence/OpenClaw-Medical-Skills

vcf-annotator

Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

chemist-analyst

Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography, mass spectrometry). Provides insights on chemical processes, material properties, reaction pathways, synthesis, and analytical methods. Use when: Chemical reactions, material analysis, synthesis planning, process optimization, environmental chemistry. Evaluates: Molecular structure, reaction mechanisms, yield, selectivity, safety, environmental impact.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

bio-alignment-io

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

sleep-analyzer

分析睡眠数据、识别睡眠模式、评估睡眠质量，并提供个性化睡眠改善建议。支持与其他健康数据的关联分析。

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

metabolomics-workbench-database

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

bio-hi-c-analysis-matrix-operations

Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.

2,009 275
Explore

Didn't find tool you were looking for?

Be as detailed as possible for better results