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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 08:33:29 +0000
parents ff2f53a32d0e
children
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5:164067a66a5c 6:5f95d385a33c
1 <!DOCTYPE HTML> 1 </div>
2 <html> 2 <div class="box">
3 <head> 3 <h4>Sequences</h4>
4 <meta charset="UTF-8"> 4 <table id="seq_info" class="inputs">
5 <title>DREME</title> 5 <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>
6 <script> 6 <th>Alphabet <div class="help" data-topic="pop_seq_alph"></div></th>
7 // @JSON_VAR data 7 <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>
8 var data = { 8 </tr>
9 "program": "dreme", 9 <tr>
10 "version": "5.0.5", 10 <td id="ins_seq_source"></td>
11 "cmd": [ 11 <td id="ins_seq_alphabet"></td>
12 "dreme", "-o", "./dreme_out", "-p", 12 <td id="ins_seq_count"></td>
13 "-norc", "-rna", "-s", "1" 13 </tr>
14 ], 14 </table>
15 "options": { 15 <script>
16 "revcomp": false, 16 {
17 "ngen": 100, 17 var db = data.sequence_db;
18 "add_pv_thresh": 0.01, 18 $("ins_seq_source").innerHTML = db.file;
19 "seed": 1, 19 $("ins_seq_alphabet").innerHTML = current_alphabet.get_alphabet_name();
20 "stop": { 20 $("ins_seq_count").innerHTML = db.count;
21 "evalue": "0.05" 21 }
22 "alphabet": { 22 </script>
23 "name": "RNA", 23 <h4>Control Sequences</h4>
24 "like": "rna", 24 <table id="seq_info" class="inputs">
25 "ncore": 4, 25 <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>
26 "symbols": [ 26 <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>
27 "background": { 27 </tr>
28 "freqs": [0.221, 0.245, 0.221, 0.312] 28 <tr>
29 "control_db": { 29 <td id="ins_cseq_source"></td>
30 "name": "shuffled positive sequences", 30 <td id="ins_cseq_count"></td>
31 "from": "shuffled", 31 </tr>
32 "count": 1000, 32 </table>
33 "freqs": [0.221, 0.245, 0.221, 0.312] 33 <script>
34 "motifs": [ 34 {
35 "db": 0, 35 var db = data.control_db;
36 "id": "UUYUCY", 36 if (db.from == "shuffled") {
37 "alt": "DREME-1", 37 $("ins_cseq_source").innerHTML = "Shuffled Sequences";
38 "len": 6, 38 } else {
39 "nsites": 459, 39 $("ins_cseq_source").innerHTML = db.file;
40 "evalue": "1.2e-013", 40 }
41 "p": 387, 41 $("ins_cseq_count").innerHTML = db.count;
42 "n": 210, 42 }
43 "pvalue": "2.6e-018", 43 </script>
44 "unerased_evalue": "1.2e-013", 44 <h4>Background</h4>
45 "pwm": [ 45 <span id="alpha_bg"></span>
46 [0.000000, 0.000000, 0.000000, 1.000000], 46 <script>
47 [0.000000, 0.000000, 0.000000, 1.000000], 47 {
48 [0.000000, 0.294118, 0.000000, 0.705882], 48 $("alpha_bg").appendChild(make_alpha_bg_table(current_alphabet, data.control_db.freqs));
49 [0.000000, 0.000000, 0.000000, 1.000000], 49 }
50 [0.000000, 1.000000, 0.000000, 0.000000], 50 </script>
51 [0.000000, 0.474946, 0.000000, 0.525054] 51 <h4>Other Settings</h4>
52 "matches": [ 52 <table id="tbl_settings" class="inputs hide_advanced">
53 "seq": "UUUUCC", 53 <tr>
54 "p": 147, 54 <th>Strand Handling</th>
55 "n": 75, 55 <td id="opt_strand">
56 "pvalue": "1.8e-007", 56 <span class="strand_none">This alphabet only has one strand</span>
57 "evalue": "8.1e-003" 57 <span class="strand_given">Only the given strand is processed</span>
58 }, { 58 <span class="strand_both">Both the given and reverse complement strands are processed</span>
59 "seq": "UUUUCU", 59 </td>
60 "p": 155, 60 </tr>
61 "n": 94, 61 <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>
62 "pvalue": "2.2e-005", 62 <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>
63 "evalue": "1.0e+000" 63 <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>
64 "seq": "UUCUCU", 64 <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>
65 "p": 94, 65 <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>
66 "n": 51, 66 </table>
67 "pvalue": "1.3e-004", 67 <script>
68 "evalue": "6.1e+000" 68 {
69 "seq": "UUCUCC", 69 $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
70 "p": 75, 70 $("opt_ngen").innerHTML = data.options.ngen;
71 "n": 42, 71 $("opt_seed").innerHTML = data.options.seed;
72 "pvalue": "1.1e-003", 72 $("opt_stop_evalue").innerHTML = data.options.stop.evalue;
73 "evalue": "5.0e+001" 73 $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");
74 <script> 74 $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");
75 var site_url = "http://meme-suite.org"; 75 }
76 </script> 76 </script>
77 /* dreme output specific css */ 77 </div>
78 /* program settings */ 78 <!-- list information on this program -->
79 </style> 79 <div id="info_sec" class="bar" style="position:relative">
80 </head> 80 <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>
81 <body data-scrollpad="true"> 81 <div class="subsection">
82 The name of the motif uses the IUPAC codes for nucleotides which has 82 <h5 id="version">DREME version</h5>
83 a different letter to represent each of the 15 possible combinations. 83 <span id="ins_version"></span>
84 The name is itself a representation of the motif though the position 84 (Release date: <span id="ins_release"></span>)<br>
85 weight matrix is not directly equivalent as it is generated from the 85 </div>
86 sites found that matched the letters given in the name. 86 <script>
87 <p>The E-value is the enrichment p-value times the number of candidate 87 $("ins_version").innerHTML = data["version"];
88 motifs tested.</p> 88 $("ins_release").innerHTML = data["release"];
89 <p>The enrichment p-value is calculated using Fisher's Exact Test for 89 </script>
90 enrichment of the motif in the positive sequences.</p> 90 <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div>
91 <p>Note that the counts used in Fisher's Exact Test are made after 91 <div class="subsection">
92 erasing sites that match previously found motifs.</p> 92 <h5 id="command">Command line</h5>
93 <p>The E-value of the motif calculated without erasing the sites of 93 <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">
94 previously found motifs.</p> 94 </textarea>
95 <p>Show more information on the motif.</p> 95 <script>$("cmd").value = data["cmd"].join(" ");</script>
96 <p>Submit your motif to another MEME Suite program or download your motif.</p> 96 </div>
97 <h5>Supported Programs</h5> 97 </div>
98 <dt>Tomtom</dt> 98
99 <dd>Tomtom is a tool for searching for similar known motifs.
100 <dt>MAST</dt>
101 <dd>MAST is a tool for searching biological sequence databases for
102 sequences that contain one or more of a group of known motifs.
103 <dt>FIMO</dt>
104 <dd>FIMO is a tool for searching biological sequence databases for
105 sequences that contain one or more known motifs.
106 <dt>GOMo</dt>
107 <dd>GOMo is a tool for identifying possible roles (Gene Ontology
108 terms) for DNA binding motifs.
109 <dt>SpaMo</dt>
110 <dd>SpaMo is a tool for inferring possible transcription factor
111 complexes by finding motifs with enriched spacings.
112 </body> 99 </body>
113 </html> 100 </html>