tooluniverse-sequence-retrieval

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

>[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:

**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" |