view test-data/dreme_output_test2.html @ 3:ec2f378ac827 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
author iuc
date Sat, 27 Nov 2021 09:45:44 +0000
parents 3e5c80594237
children f33d77dcacce
line wrap: on
line source

<!DOCTYPE HTML>
<html>
  <head>
    <meta charset="UTF-8">
    <title>DREME</title>
    <script>
      // @JSON_VAR data
      var data = {
        "program": "dreme",
        "version": "5.0.5",
        "release": "Mon Mar 18 20:12:19 2019 -0700",
        "cmd": [
          "dreme", "-o", "./dreme_out", "-p",
          "-norc", "-rna", "-s", "1", "-e", "1e-05", "-g", "100", "-mink",
          "4", "-maxk", "10"
        ],
        "options": {
          "revcomp": false,
          "ngen": 100,
          "add_pv_thresh": 0.01,
          "seed": 1,
          "stop": {
            "evalue": "1e-05"
          }
        },
        "alphabet": {
          "name": "RNA",
          "like": "rna",
          "ncore": 4,
          "symbols": [
            {
              "symbol": "A",
              "name": "Adenine",
              "colour": "CC0000"
            }, {
              "symbol": "C",
              "name": "Cytosine",
              "colour": "0000CC"
              "symbol": "G",
              "name": "Guanine",
              "colour": "FFB300"
              "symbol": "U",
              "aliases": "T",
              "name": "Uracil",
              "colour": "008000"
              "symbol": "N",
              "aliases": "X.",
              "name": "Any base",
              "equals": "ACGU"
              "symbol": "V",
              "name": "Not U",
              "equals": "ACG"
              "symbol": "H",
              "name": "Not G",
              "equals": "ACU"
              "symbol": "D",
              "name": "Not C",
              "equals": "AGU"
              "symbol": "B",
              "name": "Not A",
              "equals": "CGU"
              "symbol": "M",
              "name": "Amino",
              "equals": "AC"
              "symbol": "R",
              "name": "Purine",
              "equals": "AG"
              "symbol": "W",
              "name": "Weak",
              "equals": "AU"
              "symbol": "S",
              "name": "Strong",
              "equals": "CG"
              "symbol": "Y",
              "name": "Pyrimidine",
              "equals": "CU"
              "symbol": "K",
              "name": "Keto",
              "equals": "GU"
        "background": {
          "freqs": [0.221, 0.245, 0.221, 0.312]
        "sequence_db": {
          "count": 1000
        "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": "3.3e-013",
            "p": 387,
            "n": 210,
            "pvalue": "2.6e-018",
            "unerased_evalue": "3.3e-013",
            "pwm": [
              [0.000000, 0.000000, 0.000000, 1.000000], 
              [0.000000, 0.000000, 0.000000, 1.000000], 
              [0.000000, 0.294118, 0.000000, 0.705882], 
              [0.000000, 0.000000, 0.000000, 1.000000], 
              [0.000000, 1.000000, 0.000000, 0.000000], 
              [0.000000, 0.474946, 0.000000, 0.525054]
            "matches": [
                "seq": "UUUUCC",
                "p": 147,
                "n": 75,
                "pvalue": "1.8e-007",
                "evalue": "2.2e-002"
    </script>
var site_url = "http://meme-suite.org";
//======================================================================
// end RasterizedAlphabet
//======================================================================
//======================================================================
// start LogoMetrics object
//======================================================================
 * Initialise and display the download popup.
</style>
  </head>
  <body data-scrollpad="true">
    <!--  -->
    <div id="grey_out_page" class="grey_background" style="display:none;">
        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 logo of the motif.</p>
      <p>The logo of the reverse complement motif.</p>
      <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.
    <!-- Page starts here -->
        <h1>DREME</h1>
        <h2>Discriminative Regular Expression Motif Elicitation</h2>
        For further information on how to interpret these results please access
        To get a copy of the MEME software please access 
        If you use DREME in your research please cite the following paper:<br />
          Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.
  </body>
</html>