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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
author iuc
date Sat, 09 Apr 2022 08:32:58 +0000
parents 3e5c80594237
children
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4:e383d4bc8682 5:f33d77dcacce
1 <!DOCTYPE HTML> 1 <h4>Other Settings</h4>
2 <html> 2 <table id="tbl_settings" class="inputs hide_advanced">
3 <head> 3 <tr>
4 <meta charset="UTF-8"> 4 <th>Strand Handling</th>
5 <title>DREME</title> 5 <td id="opt_strand">
6 <script> 6 <span class="strand_none">This alphabet only has one strand</span>
7 // @JSON_VAR data 7 <span class="strand_given">Only the given strand is processed</span>
8 var data = { 8 <span class="strand_both">Both the given and reverse complement strands are processed</span>
9 "program": "dreme", 9 </td>
10 "version": "5.0.5", 10 </tr>
11 "release": "Mon Mar 18 20:12:19 2019 -0700", 11 <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>
12 "cmd": [ 12 <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>
13 "dreme", "-o", "./dreme_out", "-p", 13 <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>
14 "-norc", "-rna", "-s", "1", "-e", "1e-05", "-g", "100", "-mink", 14 <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>
15 "4", "-maxk", "10" 15 <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>
16 ], 16 </table>
17 "options": { 17 <script>
18 "revcomp": false, 18 {
19 "ngen": 100, 19 $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
20 "add_pv_thresh": 0.01, 20 $("opt_ngen").innerHTML = data.options.ngen;
21 "seed": 1, 21 $("opt_seed").innerHTML = data.options.seed;
22 "stop": { 22 $("opt_stop_evalue").innerHTML = data.options.stop.evalue;
23 "evalue": "1e-05" 23 $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");
24 } 24 $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");
25 }, 25 }
26 "alphabet": { 26 </script>
27 "name": "RNA", 27 </div>
28 "like": "rna", 28 <!-- list information on this program -->
29 "ncore": 4, 29 <div id="info_sec" class="bar" style="position:relative">
30 "symbols": [ 30 <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>
31 { 31 <div class="subsection">
32 "symbol": "A", 32 <h5 id="version">DREME version</h5>
33 "name": "Adenine", 33 <span id="ins_version"></span>
34 "colour": "CC0000" 34 (Release date: <span id="ins_release"></span>)<br>
35 }, { 35 </div>
36 "symbol": "C", 36 <script>
37 "name": "Cytosine", 37 $("ins_version").innerHTML = data["version"];
38 "colour": "0000CC" 38 $("ins_release").innerHTML = data["release"];
39 "symbol": "G", 39 </script>
40 "name": "Guanine", 40 <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div>
41 "colour": "FFB300" 41 <div class="subsection">
42 "symbol": "U", 42 <h5 id="command">Command line</h5>
43 "aliases": "T", 43 <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">
44 "name": "Uracil", 44 </textarea>
45 "colour": "008000" 45 <script>$("cmd").value = data["cmd"].join(" ");</script>
46 "symbol": "N", 46 </div>
47 "aliases": "X.", 47 </div>
48 "name": "Any base", 48
49 "equals": "ACGU"
50 "symbol": "V",
51 "name": "Not U",
52 "equals": "ACG"
53 "symbol": "H",
54 "name": "Not G",
55 "equals": "ACU"
56 "symbol": "D",
57 "name": "Not C",
58 "equals": "AGU"
59 "symbol": "B",
60 "name": "Not A",
61 "equals": "CGU"
62 "symbol": "M",
63 "name": "Amino",
64 "equals": "AC"
65 "symbol": "R",
66 "name": "Purine",
67 "equals": "AG"
68 "symbol": "W",
69 "name": "Weak",
70 "equals": "AU"
71 "symbol": "S",
72 "name": "Strong",
73 "equals": "CG"
74 "symbol": "Y",
75 "name": "Pyrimidine",
76 "equals": "CU"
77 "symbol": "K",
78 "name": "Keto",
79 "equals": "GU"
80 "background": {
81 "freqs": [0.221, 0.245, 0.221, 0.312]
82 "sequence_db": {
83 "count": 1000
84 "control_db": {
85 "name": "shuffled positive sequences",
86 "from": "shuffled",
87 "count": 1000,
88 "freqs": [0.221, 0.245, 0.221, 0.312]
89 "motifs": [
90 "db": 0,
91 "id": "UUYUCY",
92 "alt": "DREME-1",
93 "len": 6,
94 "nsites": 459,
95 "evalue": "3.3e-013",
96 "p": 387,
97 "n": 210,
98 "pvalue": "2.6e-018",
99 "unerased_evalue": "3.3e-013",
100 "pwm": [
101 [0.000000, 0.000000, 0.000000, 1.000000],
102 [0.000000, 0.000000, 0.000000, 1.000000],
103 [0.000000, 0.294118, 0.000000, 0.705882],
104 [0.000000, 0.000000, 0.000000, 1.000000],
105 [0.000000, 1.000000, 0.000000, 0.000000],
106 [0.000000, 0.474946, 0.000000, 0.525054]
107 "matches": [
108 "seq": "UUUUCC",
109 "p": 147,
110 "n": 75,
111 "pvalue": "1.8e-007",
112 "evalue": "2.2e-002"
113 </script>
114 var site_url = "http://meme-suite.org";
115 //======================================================================
116 // end RasterizedAlphabet
117 //======================================================================
118 //======================================================================
119 // start LogoMetrics object
120 //======================================================================
121 * Initialise and display the download popup.
122 </style>
123 </head>
124 <body data-scrollpad="true">
125 <!-- -->
126 <div id="grey_out_page" class="grey_background" style="display:none;">
127 The name of the motif uses the IUPAC codes for nucleotides which has
128 a different letter to represent each of the 15 possible combinations.
129 The name is itself a representation of the motif though the position
130 weight matrix is not directly equivalent as it is generated from the
131 sites found that matched the letters given in the name.
132 <p>The logo of the motif.</p>
133 <p>The logo of the reverse complement motif.</p>
134 <p>The E-value is the enrichment p-value times the number of candidate
135 motifs tested.</p>
136 <p>The enrichment p-value is calculated using Fisher's Exact Test for
137 enrichment of the motif in the positive sequences.</p>
138 <p>Note that the counts used in Fisher's Exact Test are made after
139 erasing sites that match previously found motifs.</p>
140 <p>The E-value of the motif calculated without erasing the sites of
141 previously found motifs.</p>
142 <p>Show more information on the motif.</p>
143 <p>Submit your motif to another MEME Suite program or download your motif.</p>
144 <h5>Supported Programs</h5>
145 <dt>Tomtom</dt>
146 <dd>Tomtom is a tool for searching for similar known motifs.
147 <dt>MAST</dt>
148 <dd>MAST is a tool for searching biological sequence databases for
149 sequences that contain one or more of a group of known motifs.
150 <dt>FIMO</dt>
151 <dd>FIMO is a tool for searching biological sequence databases for
152 sequences that contain one or more known motifs.
153 <dt>GOMo</dt>
154 <dd>GOMo is a tool for identifying possible roles (Gene Ontology
155 terms) for DNA binding motifs.
156 <dt>SpaMo</dt>
157 <dd>SpaMo is a tool for inferring possible transcription factor
158 complexes by finding motifs with enriched spacings.
159 <!-- Page starts here -->
160 <h1>DREME</h1>
161 <h2>Discriminative Regular Expression Motif Elicitation</h2>
162 For further information on how to interpret these results please access
163 To get a copy of the MEME software please access
164 If you use DREME in your research please cite the following paper:<br />
165 Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.
166 </body> 49 </body>
167 </html> 50 </html>