Mercurial > repos > iuc > meme_dreme

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    <title>DREME</title>
    <script>
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        "program": "dreme",
        "version": "5.0.5",
        "cmd": [
          "dreme", "-o", "./dreme_out", "-p",
          "-norc", "-rna", "-s", "1"
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        "options": {
          "revcomp": false,
          "ngen": 100,
          "add_pv_thresh": 0.01,
          "seed": 1,
          "stop": {
            "evalue": "0.05"
        "alphabet": {
          "name": "RNA",
          "like": "rna",
          "ncore": 4,
          "symbols": [
        "background": {
          "freqs": [0.221, 0.245, 0.221, 0.312]
        "control_db": {
          "name": "shuffled positive sequences",
          "from": "shuffled",
          "count": 1000,
          "freqs": [0.221, 0.245, 0.221, 0.312]
        "motifs": [
            "db": 0,
            "id": "UUYUCY",
            "alt": "DREME-1",
            "len": 6,
            "nsites": 459,
            "evalue": "1.2e-013",
            "p": 387,
            "n": 210,
            "pvalue": "2.6e-018",
            "unerased_evalue": "1.2e-013",
            "pwm": [
              [0.000000, 0.000000, 0.000000, 1.000000],
              [0.000000, 0.000000, 0.000000, 1.000000],
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            "matches": [
                "seq": "UUUUCC",
                "p": 147,
                "n": 75,
                "pvalue": "1.8e-007",
                "evalue": "8.1e-003"
              }, {
                "seq": "UUUUCU",
                "p": 155,
                "n": 94,
                "pvalue": "2.2e-005",
                "evalue": "1.0e+000"
                "seq": "UUCUCU",
                "p": 94,
                "n": 51,
                "pvalue": "1.3e-004",
                "evalue": "6.1e+000"
                "seq": "UUCUCC",
                "p": 75,
                "n": 42,
                "pvalue": "1.1e-003",
                "evalue": "5.0e+001"
    <script>
var site_url = "http://meme-suite.org";
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/* program settings */
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        The name of the motif uses the IUPAC codes for nucleotides which has
        a different letter to represent each of the 15 possible combinations.
        The name is itself a representation of the motif though the position
        weight matrix is not directly equivalent as it is generated from the
        sites found that matched the letters given in the name.
      <p>The E-value is the enrichment p-value times the number of candidate
        motifs tested.</p>
      <p>The enrichment p-value is calculated using Fisher's Exact Test for
        enrichment of the motif in the positive sequences.</p>
      <p>Note that the counts used in Fisher's Exact Test are made after
        erasing sites that match previously found motifs.</p>
      <p>The E-value of the motif calculated without erasing the sites of
        previously found motifs.</p>
      <p>Show more information on the motif.</p>
      <p>Submit your motif to another MEME Suite program or download your motif.</p>
      <h5>Supported Programs</h5>
        <dt>Tomtom</dt>
        <dd>Tomtom is a tool for searching for similar known motifs.
        <dt>MAST</dt>
        <dd>MAST is a tool for searching biological sequence databases for
          sequences that contain one or more of a group of known motifs.
        <dt>FIMO</dt>
        <dd>FIMO is a tool for searching biological sequence databases for
          sequences that contain one or more known motifs.
        <dt>GOMo</dt>
        <dd>GOMo is a tool for identifying possible roles (Gene Ontology
          terms) for DNA binding motifs.
        <dt>SpaMo</dt>
        <dd>SpaMo is a tool for inferring possible transcription factor
          complexes by finding motifs with enriched spacings.
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author	iuc
date	Wed, 11 Dec 2019 18:04:55 -0500
parents	cb8a2242bf03
children	f33d77dcacce