MEME Discover Motifs

Overview

Run de novo motif discovery on a set of DNA sequences using the MEME algorithm from the MEME Suite. MEME finds overrepresented ungapped sequence patterns (motifs) that may correspond to transcription factor binding sites, splice sites, or other functional elements. Requires at least 2 FASTA sequences as input. Returns discovered motifs with consensus sequences, E-values, probability matrices, and site counts. Note: this submits a job to meme-suite.org and polls for results (typically 30-120 seconds depending on input size).

Status

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

Last probed

1d ago

Last success

1d ago

Last latency

100ms

Schema

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

{
  "properties": {
    "distribution": {
      "default": "zoops",
      "description": "Motif site distribution model. 'oops' = one per sequence, 'zoops' = zero or one per sequence (default), 'anr' = any number of repetitions.",
      "enum": [
        "oops",
        "zoops",
        "anr"
      ],
      "type": [
        "string",
        "null"
      ]
    },
    "maxw": {
      "default": 50,
      "description": "Maximum motif width in nucleotides. Default 50.",
      "type": [
        "integer",
        "null"
      ]
    },
    "minw": {
      "default": 6,
      "description": "Minimum motif width in nucleotides. Default 6.",
      "type": [
        "integer",
        "null"
      ]
    },
    "nmotifs": {
      "default": 3,
      "description": "Maximum number of motifs to find. Default 3.",
      "type": [
        "integer",
        "null"
      ]
    },
    "operation": {
      "description": "Operation type",
      "enum": [
        "discover_motifs"
      ],
      "type": "string"
    },
    "scan_rc": {
      "default": true,
      "description": "If true (default), search both strands.",
      "type": [
        "boolean",
        "null"
      ]
    },
    "sequences": {
      "description": "Multiple DNA sequences in FASTA format (minimum 2 sequences). Should contain related sequences expected to share common motifs, e.g., promoter regions of co-regulated genes.",
      "type": "string"
    }
  },
  "required": [
    "operation",
    "sequences"
  ],
  "type": "object"
}

Examples (1)

{
  "operation": "",
  "sequences": ""
}

Identifiers

Catalog ID

tu_MEME_discover_motifs

Tool name

MEME_discover_motifs

Added

2026-04-30 22:47Z

Tags

tooluniverse