MEME Tomtom Compare

Overview

Compare a query motif against known motif databases (JASPAR, HOCOMOCO, CIS-BP) using TOMTOM from the MEME Suite. Given a motif in MEME format, identifies the most similar known transcription factor binding motifs. Useful for annotating de novo discovered motifs — e.g., after running MEME motif discovery, use TOMTOM to determine which TF likely binds the discovered motif. Returns matches ranked by E-value with query/target consensus sequences. Note: this submits a job to meme-suite.org and polls for results (typically 5-20 seconds).

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed

1d ago

Last success

1d ago

Last latency

103ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "comparison_function": {
      "default": "pearson",
      "description": "Distance function for motif comparison. 'pearson' = Pearson correlation (default), 'ed' = Euclidean distance, 'sandelin' = Sandelin-Wasserman, 'allr' = average log-likelihood ratio.",
      "enum": [
        "pearson",
        "ed",
        "sandelin",
        "allr",
        "allr5"
      ],
      "type": [
        "string",
        "null"
      ]
    },
    "evalue_threshold": {
      "default": 0.5,
      "description": "E-value threshold for reporting matches. Default 0.5. Must be <= 1.0.",
      "type": [
        "number",
        "null"
      ]
    },
    "operation": {
      "description": "Operation type",
      "enum": [
        "tomtom_compare"
      ],
      "type": "string"
    },
    "query_motif": {
      "description": "Query motif in MEME format. Must include the full MEME header followed by one or more MOTIF blocks with letter-probability matrices.",
      "type": "string"
    },
    "target_db": {
      "default": "JASPAR2026_vertebrates",
      "description": "Target motif database to search against. Options: 'JASPAR2026_vertebrates' (default, recommended), 'JASPAR2026_all', 'JASPAR2024_vertebrates', 'HOCOMOCO_v12'. Use MEME_list_databases to see all options.",
      "type": [
        "string",
        "null"
      ]
    }
  },
  "required": [
    "operation",
    "query_motif"
  ],
  "type": "object"
}

Examples (1)

{
  "operation": "",
  "query_motif": "BRCA1"
}

Identifiers

Catalog ID

tu_MEME_tomtom_compare

Tool name

MEME_tomtom_compare

Added

2026-05-01 00:58Z

Tags

tooluniverse