Hocomoco Tools

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

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

Available Tools

HOCOMOCO_get_motif (Type: HocomocoTool)

Get detailed information about a specific HOCOMOCO transcription factor binding motif. Returns ge…

HOCOMOCO_get_motif tool specification

Tool Information:

  • Name: HOCOMOCO_get_motif

  • Type: HocomocoTool

  • Description: Get detailed information about a specific HOCOMOCO transcription factor binding motif. Returns gene names, UniProt IDs, TF classification, quality metrics, consensus sequence, and optionally the position weight matrix (PWM). Quality grades: A (best), B, C, D (lowest). Data sources: P (ChIP-Seq peaks), S (HT-SELEX). Example: ‘P53.H14CORE.0.P.B’ returns TP53 motif details.

Parameters:

  • motif_id (string) (required) HOCOMOCO motif identifier. Format: GENE.COLLECTION.SUBTYPE.SOURCE.QUALITY. Examples: ‘P53.H14CORE.0.P.B’, ‘CTCF.H14CORE.0.P.B’, ‘STAT3.H14CORE.0.P.B’.

  • include_pwm (boolean) (optional) Whether to include the position weight matrix (PWM) in the response. Default: false.

Example Usage:

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

HOCOMOCO_search_motifs (Type: HocomocoTool)

Search HOCOMOCO v14 for transcription factor binding motifs by gene or protein name. Returns moti…

HOCOMOCO_search_motifs tool specification

Tool Information:

  • Name: HOCOMOCO_search_motifs

  • Type: HocomocoTool

  • Description: Search HOCOMOCO v14 for transcription factor binding motifs by gene or protein name. Returns motif IDs, quality scores, consensus sequences, and TF classification. HOCOMOCO contains high-quality TF binding models derived from ChIP-Seq data for human and mouse. Complementary to JASPAR. Example: query ‘TP53’ returns P53.H14CORE.0.P.B with consensus sequence and quality grade.

Parameters:

  • query (string) (required) Gene symbol or protein name to search for TF binding motifs. Examples: ‘TP53’, ‘CTCF’, ‘STAT3’, ‘SOX2’, ‘MYC’.

Example Usage:

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