Ncbi Nucleotide Tools#

Configuration File: ncbi_nucleotide_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the ncbi_nucleotide_tools.json configuration file.

Available Tools#

NCBI_fetch_accessions (Type: NCBINucleotideSearchTool)#

Convert GenBank UIDs to accession numbers (U00096, NC_045512, etc.). Takes UIDs from NCBI_search_…

NCBI_fetch_accessions tool specification

Tool Information:

  • Name: NCBI_fetch_accessions

  • Type: NCBINucleotideSearchTool

  • Description: Convert GenBank UIDs to accession numbers (U00096, NC_045512, etc.). Takes UIDs from NCBI_search_nucleotide and returns actual accession numbers that can be used with database tools. Returns both EMBL/GenBank accessions (U*, M*, AJ*) that work with ENA Browser tools, and RefSeq accessions (NC_*, NM_*) for NCBI tools. Use this as second step after NCBI_search_nucleotide to get usable accession numbers.

Parameters:

  • operation (unknown) (optional) Operation type (fixed: fetch_accession)

  • uids (unknown) (required) GenBank UID(s) from NCBI_search_nucleotide. Can be single UID or array of UIDs.

Example Usage:

query = {
    "name": "NCBI_fetch_accessions",
    "arguments": {
        "uids": "example_value"
    }
}
result = tu.run(query)

NCBI_get_sequence (Type: NCBINucleotideSearchTool)#

Retrieve DNA/RNA sequence data from NCBI by accession number. Returns sequences in specified form…

NCBI_get_sequence tool specification

Tool Information:

  • Name: NCBI_get_sequence

  • Type: NCBINucleotideSearchTool

  • Description: Retrieve DNA/RNA sequence data from NCBI by accession number. Returns sequences in specified format (fasta, gb, embl). Works with both EMBL/GenBank accessions (U00096, M15390) and RefSeq accessions (NC_045512, NM_000546). Use this to get actual sequence data after finding accessions with NCBI_search_nucleotide. Returns full sequence with annotations depending on format.

Parameters:

  • operation (unknown) (optional) Operation type (fixed: fetch_sequence)

  • accession (string) (required) NCBI accession number (e.g., ‘U00096’, ‘NC_045512’, ‘NM_000546’). Works with GenBank, EMBL, and RefSeq accessions.

  • format (string) (optional) Sequence format: ‘fasta’ for FASTA, ‘gb’ for GenBank, ‘embl’ for EMBL, ‘gp’ for GenPept protein. Default: fasta

Example Usage:

query = {
    "name": "NCBI_get_sequence",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

NCBI_search_nucleotide (Type: NCBINucleotideSearchTool)#

Search NCBI Nucleotide (GenBank/EMBL/RefSeq) with exact offset pagination and automatically resol…

NCBI_search_nucleotide tool specification

Tool Information:

  • Name: NCBI_search_nucleotide

  • Type: NCBINucleotideSearchTool

  • Description: Search NCBI Nucleotide (GenBank/EMBL/RefSeq) with exact offset pagination and automatically resolve each returned UID to an accession. The response reports count, returned, has_more, and next_offset; continue with offset=next_offset until has_more is false. Supports organism, gene, strain, sequence type, title keywords, or a free-form NCBI query.

Parameters:

  • operation (unknown) (optional) Operation type (fixed: search)

  • organism (string) (optional) Organism name to search (e.g., ‘Escherichia coli’, ‘Homo sapiens’). Searches in [Organism] field.

  • gene (string) (optional) Gene name to search (e.g., ‘BRCA1’, ‘TP53’). Searches in [Gene] field.

  • strain (string) (optional) Strain name to filter (e.g., ‘K-12’, ‘MG1655’). Searches in [Strain] field.

  • keywords (string) (optional) Keywords to search in titles (e.g., ‘complete genome’, ‘mitochondrial’). Searches in [Title] field.

  • seq_type (string) (optional) Sequence type filter: ‘complete_genome’ for complete genomes, ‘mrna’ for mRNA sequences, ‘refseq’ for RefSeq curated sequences

  • query (string) (optional) Free-form search query if not using structured filters. Use NCBI query syntax (e.g., ‘(Escherichia coli[Organism]) AND (K-12[Strain])’)

  • limit (integer) (optional) Page size (1-100).

  • offset (integer) (optional) Zero-based result offset, mapped to NCBI ESearch retstart. Continue with data.next_offset.

  • sort (string) (optional) Sort order for results (default: relevance). pub_date sorts by NCBI’s ‘Date Released’, length by ‘Sequence Length’.

Example Usage:

query = {
    "name": "NCBI_search_nucleotide",
    "arguments": {
    }
}
result = tu.run(query)