Meme Tools

Configuration File: meme_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

MEME_discover_motifs (Type: MEMETool)

Run de novo motif discovery on a set of DNA sequences using the MEME algorithm from the MEME Suit…

MEME_discover_motifs tool specification

Tool Information:

  • Name: MEME_discover_motifs

  • Type: MEMETool

  • Description: 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).

Parameters:

  • operation (string) (required) Operation type

  • sequences (string) (required) 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.

  • nmotifs ([‘integer’, ‘null’]) (optional) Maximum number of motifs to find. Default 3.

  • minw ([‘integer’, ‘null’]) (optional) Minimum motif width in nucleotides. Default 6.

  • maxw ([‘integer’, ‘null’]) (optional) Maximum motif width in nucleotides. Default 50.

  • distribution ([‘string’, ‘null’]) (optional) Motif site distribution model. ‘oops’ = one per sequence, ‘zoops’ = zero or one per sequence (default), ‘anr’ = any number of repetitions.

  • scan_rc ([‘boolean’, ‘null’]) (optional) If true (default), search both strands.

Example Usage:

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

MEME_fimo_scan (Type: MEMETool)

Scan DNA sequences for transcription factor (TF) binding motifs using FIMO (Find Individual Motif…

MEME_fimo_scan tool specification

Tool Information:

  • Name: MEME_fimo_scan

  • Type: MEMETool

  • Description: 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).

Parameters:

  • operation (string) (required) Operation type

  • sequences (string) (required) DNA sequences in FASTA format to scan for motif occurrences. Example: ‘>seq1nATGCATGCTATAAAAGGATCCn>seq2nGGATCCATGCATGCATGCAT’

  • motif_text (string) (required) 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 5nnALPHABET= ACGTnnstrands: + -nnBackground letter frequenciesnA 0.25 C 0.25 G 0.25 T 0.25nnMOTIF TATABOXnletter-probability matrix: alength= 4 w= 6 nsites= 100 E= 0n0.00 0.00 0.00 1.00n1.00 0.00 0.00 0.00n0.00 0.00 0.00 1.00n1.00 0.00 0.00 0.00n1.00 0.00 0.00 0.00n1.00 0.00 0.00 0.00’

  • pvalue_threshold ([‘number’, ‘null’]) (optional) P-value threshold for reporting motif occurrences. Default 1e-4. Lower values are more stringent.

  • scan_rc ([‘boolean’, ‘null’]) (optional) If true (default), scan both strands. Set false to scan only the given strand.

Example Usage:

query = {
    "name": "MEME_fimo_scan",
    "arguments": {
        "operation": "example_value",
        "sequences": "example_value",
        "motif_text": "example_value"
    }
}
result = tu.run(query)

MEME_list_databases (Type: MEMETool)

List available motif databases on the MEME Suite server for use with FIMO motif scanning and TOMT…

MEME_list_databases tool specification

Tool Information:

  • Name: MEME_list_databases

  • Type: MEMETool

  • Description: List available motif databases on the MEME Suite server for use with FIMO motif scanning and TOMTOM motif comparison. Returns categories (Eukaryote DNA, JASPAR, HOCOMOCO, CIS-BP, etc.) with database counts, plus shortcut names for popular databases that can be used directly with the TOMTOM target_db parameter. No remote API call is needed — this returns locally cached database metadata.

Parameters:

  • operation (string) (required) Operation type

  • category_filter ([‘string’, ‘null’]) (optional) Filter categories by name or description substring. E.g., ‘JASPAR’, ‘human’, ‘RNA’. If null, returns all categories.

Example Usage:

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

MEME_tomtom_compare (Type: MEMETool)

Compare a query motif against known motif databases (JASPAR, HOCOMOCO, CIS-BP) using TOMTOM from …

MEME_tomtom_compare tool specification

Tool Information:

  • Name: MEME_tomtom_compare

  • Type: MEMETool

  • Description: 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).

Parameters:

  • operation (string) (required) Operation type

  • query_motif (string) (required) Query motif in MEME format. Must include the full MEME header followed by one or more MOTIF blocks with letter-probability matrices.

  • target_db ([‘string’, ‘null’]) (optional) 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.

  • evalue_threshold ([‘number’, ‘null’]) (optional) E-value threshold for reporting matches. Default 0.5. Must be <= 1.0.

  • comparison_function ([‘string’, ‘null’]) (optional) Distance function for motif comparison. ‘pearson’ = Pearson correlation (default), ‘ed’ = Euclidean distance, ‘sandelin’ = Sandelin-Wasserman, ‘allr’ = average log-likelihood ratio.

Example Usage:

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