Mercurial > repos > iuc > meme_psp_gen
comparison test-data/dreme_output_test2.html @ 6:5f95d385a33c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
author | iuc |
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date | Sat, 09 Apr 2022 08:33:29 +0000 |
parents | ff2f53a32d0e |
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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> |