Cortexa research tool·genomics·meme

MEME Fimo Scan

Scan DNA sequences for transcription factor (TF) binding motifs using FIMO (Find Individual Motif Occurrences) from the MEME Suite. Provide sequences in FASTA format and a motif in MEME format, and FIMO returns all statistically significant binding sites with p-values, scores, strand, and matched sequences. Ideal for scanning promoter regions for known TF binding sites from JASPAR or HOCOMOCO. Note: this submits a job to meme-suite.org and polls for results (typically 10-30 seconds).

Livelast probed 2026-04-30 23:07Z· 106msCortexa

Status

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

Last probed: 1d ago
Last success: 1d ago
Last latency: 106ms

Schema

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

{
  "properties": {
    "motif_text": {
      "description": "Motif(s) in MEME format. Must include the full MEME header (MEME version 5, ALPHABET, strands, Background letter frequencies) followed by MOTIF blocks with letter-probability matrices. Example for a TATA box motif: 'MEME version 5\\n\\nALPHABET= ACGT\\n\\nstrands: + -\\n\\nBackground letter frequencies\\nA 0.25 C 0.25 G 0.25 T 0.25\\n\\nMOTIF TATABOX\\nletter-probability matrix: alength= 4 w= 6 nsites= 100 E= 0\\n0.00 0.00 0.00 1.00\\n1.00 0.00 0.00 0.00\\n0.00 0.00 0.00 1.00\\n1.00 0.00 0.00 0.00\\n1.00 0.00 0.00 0.00\\n1.00 0.00 0.00 0.00'",
      "type": "string"
    },
    "operation": {
      "description": "Operation type",
      "enum": [
        "fimo_scan"
      ],
      "type": "string"
    },
    "pvalue_threshold": {
      "default": 0.0001,
      "description": "P-value threshold for reporting motif occurrences. Default 1e-4. Lower values are more stringent.",
      "type": [
        "number",
        "null"
      ]
    },
    "scan_rc": {
      "default": true,
      "description": "If true (default), scan both strands. Set false to scan only the given strand.",
      "type": [
        "boolean",
        "null"
      ]
    },
    "sequences": {
      "description": "DNA sequences in FASTA format to scan for motif occurrences. Example: '>seq1\\nATGCATGCTATAAAAGGATCC\\n>seq2\\nGGATCCATGCATGCATGCAT'",
      "type": "string"
    }
  },
  "required": [
    "operation",
    "sequences",
    "motif_text"
  ],
  "type": "object"
}

Examples (1)

Default MEME Fimo Scan call

public-safeinput

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

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_MEME_fimo_scan
Tool name: MEME_fimo_scan
Added: 2026-04-30 22:47Z
Tags: tooluniverse

MEME Fimo Scan

Livelast probed 2026-04-30 23:07Z· 106msCortexa

Schema

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

{ "properties": { "motif_text": { "description": "Motif(s) in MEME format. Must include the full MEME header (MEME version 5, ALPHABET, strands, Background letter frequencies) followed by MOTIF blocks with letter-probability matrices. Example for a TATA box motif: 'MEME version 5\\n\\nALPHABET= ACGT\\n\\nstrands: + -\\n\\nBackground letter frequencies\\nA 0.25 C 0.25 G 0.25 T 0.25\\n\\nMOTIF TATABOX\\nletter-probability matrix: alength= 4 w= 6 nsites= 100 E= 0\\n0.00 0.00 0.00 1.00\\n1.00 0.00 0.00 0.00\\n0.00 0.00 0.00 1.00\\n1.00 0.00 0.00 0.00\\n1.00 0.00 0.00 0.00\\n1.00 0.00 0.00 0.00'", "type": "string" }, "operation": { "description": "Operation type", "enum": [ "fimo_scan" ], "type": "string" }, "pvalue_threshold": { "default": 0.0001, "description": "P-value threshold for reporting motif occurrences. Default 1e-4. Lower values are more stringent.", "type": [ "number", "null" ] }, "scan_rc": { "default": true, "description": "If true (default), scan both strands. Set false to scan only the given strand.", "type": [ "boolean", "null" ] }, "sequences": { "description": "DNA sequences in FASTA format to scan for motif occurrences. Example: '>seq1\\nATGCATGCTATAAAAGGATCC\\n>seq2\\nGGATCCATGCATGCATGCAT'", "type": "string" } }, "required": [ "operation", "sequences", "motif_text" ], "type": "object" }