Ensembl Tools

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

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

Available Tools

ensembl_get_sequence (Type: EnsemblGetSequence)

Get DNA sequence for a gene, transcript, or genomic region. Returns sequence in FASTA format.

ensembl_get_sequence tool specification

Tool Information:

  • Name: ensembl_get_sequence

  • Type: EnsemblGetSequence

  • Description: Get DNA sequence for a gene, transcript, or genomic region. Returns sequence in FASTA format.

Parameters:

  • sequence_id (string) (required) Ensembl gene/transcript ID or genomic region (e.g., ‘ENSG00000139618’ or ‘1:1000000-2000000’)

  • type (string) (optional) Sequence type: ‘genomic’, ‘cds’, ‘cdna’, ‘peptide’

Example Usage:

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

ensembl_get_variants (Type: EnsemblGetVariants)

Get genetic variants in a genomic region. Returns SNP and indel information.

ensembl_get_variants tool specification

Tool Information:

  • Name: ensembl_get_variants

  • Type: EnsemblGetVariants

  • Description: Get genetic variants in a genomic region. Returns SNP and indel information.

Parameters:

  • region (string) (required) Genomic region in format ‘chromosome:start-end’ (e.g., ‘13:32315086-32400268’)

  • species (string) (optional) Species name

Example Usage:

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

ensembl_lookup_gene (Type: EnsemblLookupGene)

Lookup gene information by Ensembl gene ID or symbol. Returns gene details including location, de…

ensembl_lookup_gene tool specification

Tool Information:

  • Name: ensembl_lookup_gene

  • Type: EnsemblLookupGene

  • Description: Lookup gene information by Ensembl gene ID or symbol. Returns gene details including location, description, and external references.

Parameters:

  • gene_id (string) (required) Ensembl gene ID or symbol (e.g., ‘ENSG00000139618’ or ‘BRCA1’)

Example Usage:

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