Ensembl Compara Tools#

Configuration File: ensembl_compara_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

EnsemblCompara_get_cafe_tree (Type: EnsemblComparaTool)#

Retrieve an Ensembl Compara CAFE gene-family gain/loss tree. Nodes are recoverably paginated with…

EnsemblCompara_get_cafe_tree tool specification

Tool Information:

  • Name: EnsemblCompara_get_cafe_tree

  • Type: EnsemblComparaTool

  • Description: Retrieve an Ensembl Compara CAFE gene-family gain/loss tree. Nodes are recoverably paginated with limit/offset and a complete total_nodes count; continue with data.next_offset while data.has_more is true. The recursive collector has no hidden cap.

Parameters:

  • gene_tree_id ([‘string’, ‘null’]) (optional) Ensembl gene tree (family) stable ID, e.g. ‘ENSGT00390000003602’. Use this OR ‘gene’.

  • gene ([‘string’, ‘null’]) (optional) Gene symbol (e.g. ‘BRCA2’) or Ensembl gene ID (e.g. ‘ENSG00000139618’). The CAFE tree for the family containing this gene is returned. Use this OR ‘gene_tree_id’.

  • species ([‘string’, ‘null’]) (optional) Species for symbol lookup when ‘gene’ is a symbol (default: ‘human’). Examples: ‘human’, ‘mouse’, ‘homo_sapiens’.

  • limit (integer) (optional) Maximum CAFE nodes per page (default 200).

  • offset (integer) (optional) Zero-based node offset. Continue with data.next_offset.

Example Usage:

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

EnsemblCompara_get_gene_tree (Type: EnsemblComparaTool)#

Get an Ensembl Compara phylogenetic gene tree and its complete member count. Members are recovera…

EnsemblCompara_get_gene_tree tool specification

Tool Information:

  • Name: EnsemblCompara_get_gene_tree

  • Type: EnsemblComparaTool

  • Description: Get an Ensembl Compara phylogenetic gene tree and its complete member count. Members are recoverably paginated with limit/offset; continue with data.next_offset while data.has_more is true. The collector itself has no hidden cap.

Parameters:

  • gene (string) (required) Gene symbol or Ensembl gene ID. Examples: ‘TP53’, ‘BRCA1’, ‘ENSG00000141510’. Ensembl IDs are more reliable than symbols for gene tree retrieval.

  • species (string) (optional) Species (default: ‘human’). Used when providing a gene symbol. Examples: ‘human’, ‘mouse’.

  • limit (integer) (optional) Maximum tree members per page (default 50).

  • offset (integer) (optional) Zero-based member offset. Continue with data.next_offset.

Example Usage:

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

EnsemblCompara_get_orthologues (Type: EnsemblComparaTool)#

Find orthologous genes (genes in different species that evolved from a common ancestor) using Ens…

EnsemblCompara_get_orthologues tool specification

Tool Information:

  • Name: EnsemblCompara_get_orthologues

  • Type: EnsemblComparaTool

  • Description: Find orthologous genes (genes in different species that evolved from a common ancestor) using Ensembl Compara. Essential for comparative genomics - finding the mouse, zebrafish, or fly equivalent of a human gene. Returns orthologue gene IDs, species, homology type (one-to-one, one-to-many), and taxonomy level of divergence. Example: TP53 in human has a one-to-one orthologue (Trp53) in mouse.

Parameters:

  • gene (string) (required) Gene symbol or Ensembl gene ID. Examples: ‘BRCA1’, ‘TP53’, ‘ENSG00000141510’, ‘ENSG00000012048’.

  • species (string) (optional) Source species (default: ‘human’). Examples: ‘human’, ‘mouse’, ‘zebrafish’, ‘drosophila_melanogaster’.

  • target_species (string) (optional) Target species to limit orthologue search. Examples: ‘mouse’, ‘zebrafish’, ‘rat’, ‘drosophila_melanogaster’. Default: all species.

  • target_taxon (integer) (optional) NCBI taxon ID to limit orthologue search. Examples: 10090 (mouse), 7955 (zebrafish), 7227 (fruit fly). Alternative to target_species.

Example Usage:

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

EnsemblCompara_get_paralogues (Type: EnsemblComparaTool)#

Find paralogous genes (genes within the same species that arose from gene duplication events) usi…

EnsemblCompara_get_paralogues tool specification

Tool Information:

  • Name: EnsemblCompara_get_paralogues

  • Type: EnsemblComparaTool

  • Description: Find paralogous genes (genes within the same species that arose from gene duplication events) using Ensembl Compara. Paralogues often have related but diverged functions. Returns paralogue gene IDs, duplication type, and evolutionary context. Example: TP53 has paralogues TP63 (ENSG00000073282) and TP73 (ENSG00000078900) in human, from ancient vertebrate gene duplication.

Parameters:

  • gene (string) (required) Gene symbol or Ensembl gene ID. Examples: ‘TP53’, ‘BRCA1’, ‘ENSG00000141510’.

  • species (string) (optional) Species (default: ‘human’). Examples: ‘human’, ‘mouse’, ‘zebrafish’.

Example Usage:

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