Ensembl Sequence Tools

Configuration File: ensembl_sequence_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

EnsemblSeq_get_id_sequence (Type: EnsemblSequenceTool)

Get the amino acid or nucleotide sequence for an Ensembl ID (protein, transcript, or gene). Retri…

EnsemblSeq_get_id_sequence tool specification

Tool Information:

  • Name: EnsemblSeq_get_id_sequence

  • Type: EnsemblSequenceTool

  • Description: Get the amino acid or nucleotide sequence for an Ensembl ID (protein, transcript, or gene). Retrieves protein sequences from ENSP IDs, cDNA/CDS from ENST IDs, or genomic DNA from ENSG IDs. Example: ENSP00000269305 returns the 393 amino acid protein sequence of TP53 canonical isoform. ENST00000269305 with type=’cdna’ returns the 2512 bp cDNA sequence of TP53-201.

Parameters:

  • ensembl_id (string) (required) Ensembl stable ID. Examples: ‘ENSP00000269305’ (TP53 protein, 393 aa), ‘ENST00000269305’ (TP53-201 transcript), ‘ENSG00000141510’ (TP53 gene). Protein IDs start with ENSP, transcript with ENST, gene with ENSG.

  • type (string) (optional) Sequence type to return. Options: ‘protein’ (amino acid), ‘cdna’ (spliced cDNA), ‘cds’ (coding sequence), ‘genomic’ (unspliced DNA). Default: ‘protein’ for ENSP IDs, auto-detected for others.

Example Usage:

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

EnsemblSeq_get_region_sequence (Type: EnsemblSequenceTool)

Get the DNA nucleotide sequence for a specific genomic region from Ensembl. Retrieves the referen…

EnsemblSeq_get_region_sequence tool specification

Tool Information:

  • Name: EnsemblSeq_get_region_sequence

  • Type: EnsemblSequenceTool

  • Description: Get the DNA nucleotide sequence for a specific genomic region from Ensembl. Retrieves the reference genome sequence for given chromosome coordinates. Useful for examining regulatory regions, intergenic sequences, or any arbitrary genomic interval. Example: region ‘17:7668421-7668520’ in homo_sapiens returns 100 bp of the TP53 locus. Supports any Ensembl species and coordinate strand.

Parameters:

  • region (string) (required) Genomic region in format ‘chr:start-end’ or ‘chr:start..end:strand’. Examples: ‘17:7668421-7668520’ (TP53 locus, 100bp), ‘7:140424943-140425043’ (BRAF locus, 100bp), ‘X:15560138-15602945’ (MECP2 gene). Strand: 1 for forward, -1 for reverse.

  • species (string) (optional) Ensembl species name. Default: ‘homo_sapiens’. Examples: ‘mus_musculus’, ‘danio_rerio’, ‘drosophila_melanogaster’.

Example Usage:

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