Cortexa research tool·genomics·ncbi_nucleotide

NCBI Search Nucleotide

Search NCBI Nucleotide database (GenBank/EMBL/RefSeq) by organism, gene name, or keywords. Returns GenBank UIDs which can be used to fetch accession numbers. Supports filtering by organism, gene, strain, sequence type (complete genome, mRNA, RefSeq). Use this to discover DNA/RNA sequences for specific organisms or genes. Returns both EMBL/GenBank accessions (U00096, M15390) and RefSeq accessions (NC_*, NM_*). Follow up with NCBI_fetch_accessions to get actual accession numbers.

Livelast probed 2026-04-30 23:07Z· 121msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 121ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "gene": {
      "description": "Gene name to search (e.g., 'BRCA1', 'TP53'). Searches in [Gene] field.",
      "type": "string"
    },
    "keywords": {
      "description": "Keywords to search in titles (e.g., 'complete genome', 'mitochondrial'). Searches in [Title] field.",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of results to return (default: 20, max: 100)",
      "maximum": 100,
      "minimum": 1,
      "type": "integer"
    },
    "operation": {
      "const": "search",
      "description": "Operation type (fixed: search)"
    },
    "organism": {
      "description": "Organism name to search (e.g., 'Escherichia coli', 'Homo sapiens'). Searches in [Organism] field.",
      "type": "string"
    },
    "query": {
      "description": "Free-form search query if not using structured filters. Use NCBI query syntax (e.g., '(Escherichia coli[Organism]) AND (K-12[Strain])')",
      "type": "string"
    },
    "seq_type": {
      "description": "Sequence type filter: 'complete_genome' for complete genomes, 'mrna' for mRNA sequences, 'refseq' for RefSeq curated sequences",
      "enum": [
        "complete_genome",
        "mrna",
        "refseq"
      ],
      "type": "string"
    },
    "sort": {
      "default": "relevance",
      "description": "Sort order for results (default: relevance)",
      "enum": [
        "relevance",
        "pub_date",
        "title"
      ],
      "type": "string"
    },
    "strain": {
      "description": "Strain name to filter (e.g., 'K-12', 'MG1655'). Searches in [Strain] field.",
      "type": "string"
    }
  },
  "required": [],
  "type": "object"
}

Examples (1)

Default NCBI Search Nucleotide call

public-safeinput

{
  "gene": "BRCA1",
  "limit": 3,
  "query": "BRCA1"
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_NCBI_search_nucleotide
Tool name: NCBI_search_nucleotide
Added: 2026-04-30 22:47Z
Tags: tooluniverse

NCBI Search Nucleotide

Livelast probed 2026-04-30 23:07Z· 121msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "gene": { "description": "Gene name to search (e.g., 'BRCA1', 'TP53'). Searches in [Gene] field.", "type": "string" }, "keywords": { "description": "Keywords to search in titles (e.g., 'complete genome', 'mitochondrial'). Searches in [Title] field.", "type": "string" }, "limit": { "default": 20, "description": "Maximum number of results to return (default: 20, max: 100)", "maximum": 100, "minimum": 1, "type": "integer" }, "operation": { "const": "search", "description": "Operation type (fixed: search)" }, "organism": { "description": "Organism name to search (e.g., 'Escherichia coli', 'Homo sapiens'). Searches in [Organism] field.", "type": "string" }, "query": { "description": "Free-form search query if not using structured filters. Use NCBI query syntax (e.g., '(Escherichia coli[Organism]) AND (K-12[Strain])')", "type": "string" }, "seq_type": { "description": "Sequence type filter: 'complete_genome' for complete genomes, 'mrna' for mRNA sequences, 'refseq' for RefSeq curated sequences", "enum": [ "complete_genome", "mrna", "refseq" ], "type": "string" }, "sort": { "default": "relevance", "description": "Sort order for results (default: relevance)", "enum": [ "relevance", "pub_date", "title" ], "type": "string" }, "strain": { "description": "Strain name to filter (e.g., 'K-12', 'MG1655'). Searches in [Strain] field.", "type": "string" } }, "required": [], "type": "object" }