首页/数据 & AI/tooluniverse-sequence-retrieval
T

tooluniverse-sequence-retrieval

by @mims-harvardv1.0.0
0.0(0)

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, pro

Information RetrievalSequence ModelsNLPMachine LearningData MiningGitHub
安装方式
npx skills add mims-harvard/tooluniverse --skill tooluniverse-sequence-retrieval
compare_arrows

Before / After 效果对比

0 组

description 文档

name: tooluniverse-sequence-retrieval description: 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.

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

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

# 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

# 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)

# 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.

# 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

# 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"

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"

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" |

forum用户评价 (0)

发表评价

效果
易用性
文档
兼容性

暂无评价，来写第一条吧

统计数据

安装量1.3K
评分0.0 / 5.0
版本1.0.0
更新日期2026年3月16日
对比案例0 组

用户评分

0.0(0)
5
0%
4
0%
3
0%
2
0%
1
0%

为此 Skill 评分

0.0

兼容平台

🔧Claude Code

时间线

创建2026年3月16日
最后更新2026年3月16日