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). When include_pwm=true, PWM retrieval and shape validation are mandatory: an unavailable or malformed matrix returns an explicit error rather than a successful metadata-only record. The returned motif identity must exactly match motif_id. Quality grades: A (best), B, C, D (lowest). Data sources: P (ChIP-Seq peaks), S (HT-SELEX).

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 require and include the position weight matrix (PWM). If true, the tool fails explicitly unless the PWM contains model_length rows of four numeric values.

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. Use offset/limit and the metadata next_offset value to retrieve every match; broad searches such as FOX or ZNF return more than one page. Metadata reports total, returned, has_more, and any motif IDs whose detail request failed. HOCOMOCO contains high-quality TF binding models derived from ChIP-Seq data for human and mouse. Complementary to JASPAR.

Parameters:

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

  • offset (integer) (optional) Zero-based offset into all matching HOCOMOCO motif IDs. Use metadata.next_offset to request the next page.

  • limit (integer) (optional) Number of motif details to retrieve for this page. Each item requires a separate HOCOMOCO detail request.

Example Usage:

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