Ensembl Regulation Tools#

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

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

Available Tools#

EnsemblReg_get_binding_matrix (Type: EnsemblRegulationTool)#

Get a transcription factor binding matrix (position weight matrix/PWM) by stable ID from the Ense…

EnsemblReg_get_binding_matrix tool specification

Tool Information:

  • Name: EnsemblReg_get_binding_matrix

  • Type: EnsemblRegulationTool

  • Description: Get a transcription factor binding matrix (position weight matrix/PWM) by stable ID from the Ensembl REST API. Returns the nucleotide frequency matrix, threshold, associated TF complexes, and consensus sequence. Binding matrices describe the DNA sequence preferences of transcription factors and are essential for predicting TF binding sites and understanding gene regulation. Example: ENSPFM0320 returns the PAX5 binding matrix with 18 positions.

Parameters:

  • species (string) (optional) Species name. Use ‘homo_sapiens’ for human. Default: ‘homo_sapiens’.

  • binding_matrix_id (string) (required) Ensembl binding matrix stable ID. Format: ‘ENSPFM0XXX’. Examples: ‘ENSPFM0320’ (PAX5), ‘ENSPFM0423’ (NR2F1), ‘ENSPFM0001’ (ALX3).

Example Usage:

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

EnsemblReg_get_constrained_elements (Type: EnsemblRegulationTool)#

Get and page through evolutionarily constrained elements in a genomic region from Ensembl Compara…

EnsemblReg_get_constrained_elements tool specification

Tool Information:

  • Name: EnsemblReg_get_constrained_elements

  • Type: EnsemblRegulationTool

  • Description: Get and page through evolutionarily constrained elements in a genomic region from Ensembl Compara. Returns the true element count and explicit continuation metadata so dense regions do not silently stop at 200 records. Results remain ordered by descending conservation score.

Parameters:

  • species (string) (optional) Species name. Use ‘homo_sapiens’ for human. Default: ‘homo_sapiens’.

  • region (string) (required) Genomic region in format ‘chromosome:start-end’. Example: ‘17:7661779-7687538’ for TP53, ‘7:140424943-140624564’ for BRAF.

  • limit (integer) (optional) Maximum constrained elements to return on this page.

  • offset (integer) (optional) Zero-based offset into score-sorted constrained elements.

Example Usage:

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

EnsemblReg_get_motif_features (Type: EnsemblRegulationTool)#

Get and page through transcription factor (TF) binding motif features in a genomic region from th…

EnsemblReg_get_motif_features tool specification

Tool Information:

  • Name: EnsemblReg_get_motif_features

  • Type: EnsemblRegulationTool

  • Description: Get and page through transcription factor (TF) binding motif features in a genomic region from the Ensembl REST API. Returns the true motif count and explicit continuation metadata so dense regions do not silently stop at 200 records, plus binding matrix IDs, TF complex names, scores, and genomic positions.

Parameters:

  • species (string) (optional) Species name. Use ‘homo_sapiens’ for human, ‘mus_musculus’ for mouse. Default: ‘homo_sapiens’.

  • region (string) (required) Genomic region in format ‘chromosome:start-end’. Example: ‘7:140424943-140524564’ for the BRAF locus, ‘17:7661779-7687538’ for the TP53 locus.

  • limit (integer) (optional) Maximum motif features to return on this page.

  • offset (integer) (optional) Zero-based offset into all matching motif features.

Example Usage:

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