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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:10:48 -0400
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1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2 <html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme">
3 <head>
4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
5 <meta charset="UTF-8">
6 <title>FIMO Results</title>
7 <style type="text/css">
8 td.left {text-align: left;}
9 td.right {text-align: right; padding-right: 1cm;}
10 </style>
11 </head>
12 <body bgcolor="#D5F0FF">
13 <a name="top_buttons"></a>
14 <hr>
15 <table summary="buttons" align="left" cellspacing="0">
16 <tr>
17 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
18 <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
19 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
20 </tr>
21 </table>
22 <br/>
23 <br/>
24 <hr/>
25 <center><big><b>FIMO - Motif search tool</b></big></center>
26 <hr>
27 <p>
28 FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)
29 </p>
30 <p>
31 For further information on how to interpret these results
32 or to get a copy of the FIMO software please access
33 <a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>
34 <p>If you use FIMO in your research, please cite the following paper:<br>
35 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
36 "FIMO: Scanning for occurrences of a given motif",
37 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
38 <a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p>
39 <hr>
40 <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
41 <hr>
42 <div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
43 <p>
44 DATABASE hsa_chrM.fa
45 <br />
46 Database contains 1 sequences, 16569 residues
47 </p>
48 <p>
49 MOTIFS meme_fimo_input_1.xml (DNA)
50 <table>
51 <thead>
52 <tr>
53 <th style="border-bottom: 1px dashed;">MOTIF</th>
54 <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
55 <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >
56 BEST POSSIBLE MATCH
57 </th>
58 </tr>
59 </thead>
60 <tbody>
61 <tr>
62 <td style="text-align:right;">TACTAAYM</td>
63 <td style="text-align:right;padding-left: 1em;">8</td>
64 <td style="text-align:left;padding-left: 1em;">TACTAACA</td>
65 </tr>
66 </tbody>
67 </table>
68 </p>
69 <p>
70 Random model letter frequencies (--nrdb--):
71 <br/>
72
73 A 0.275 C 0.225 G 0.225 T 0.275 </p>
74 </div>
75 <hr>
76 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
77 <hr>
78 <ul>
79 <li>
80 There were 11 motif occurences with a p-value less than 0.0001.
81
82 The full set of motif occurences can be seen in the
83 tab-delimited plain text output file
84 <a href="fimo.txt">fimo.txt</a>,
85 the GFF file
86 <a href="fimo.gff">fimo.gff</a>
87 which may be suitable for uploading to the
88 <a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
89 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
90 or the XML file
91 <a href="fimo.xml">fimo.xml</a>.
92 </li>
93 <li>
94 The p-value of a motif occurrence is defined as the
95 probability of a random sequence of the same length as the motif
96 matching that position of the sequence with as good or better a score.
97 </li>
98 <li>
99 The score for the match of a position in a sequence to a motif
100 is computed by summing the appropriate entries from each column of
101 the position-dependent scoring matrix that represents the motif.
102 </li>
103 <li>
104 The q-value of a motif occurrence is defined as the
105 false discovery rate if the occurrence is accepted as significant.
106 </li>
107 <li>The table is sorted by increasing p-value.</li>
108 </ul>
109 <table border="1">
110 <thead>
111 <tr>
112 <th>Motif ID</th>
113 <th>Alt ID</th>
114 <th>Sequence Name</th>
115 <th>Strand</th>
116 <th>Start</th>
117 <th>End</th>
118 <th>p-value</th>
119 <th>q-value</th>
120 <th>Matched Sequence</th>
121 </tr>
122 </thead>
123 <tbody>
124 <tr>
125 <td style="text-align:left;">TACTAAYM</td>
126 <td style="text-align:left;">MEME-1</td>
127 <td style="text-align:left;">chrM</td>
128 <td style="text-align:center;">-</td>
129 <td style="text-align:left;">2299</td>
130 <td style="text-align:left;">2306</td>
131 <td style="text-align:left;">2.18e-05</td>
132 <td style="text-align:left;">0.142</td>
133 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
134 </tr>
135 <tr>
136 <td style="text-align:left;">TACTAAYM</td>
137 <td style="text-align:left;">MEME-1</td>
138 <td style="text-align:left;">chrM</td>
139 <td style="text-align:center;">+</td>
140 <td style="text-align:left;">6529</td>
141 <td style="text-align:left;">6536</td>
142 <td style="text-align:left;">2.18e-05</td>
143 <td style="text-align:left;">0.142</td>
144 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
145 </tr>
146 <tr>
147 <td style="text-align:left;">TACTAAYM</td>
148 <td style="text-align:left;">MEME-1</td>
149 <td style="text-align:left;">chrM</td>
150 <td style="text-align:center;">+</td>
151 <td style="text-align:left;">7741</td>
152 <td style="text-align:left;">7748</td>
153 <td style="text-align:left;">2.18e-05</td>
154 <td style="text-align:left;">0.142</td>
155 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
156 </tr>
157 <tr>
158 <td style="text-align:left;">TACTAAYM</td>
159 <td style="text-align:left;">MEME-1</td>
160 <td style="text-align:left;">chrM</td>
161 <td style="text-align:center;">+</td>
162 <td style="text-align:left;">13656</td>
163 <td style="text-align:left;">13663</td>
164 <td style="text-align:left;">2.18e-05</td>
165 <td style="text-align:left;">0.142</td>
166 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
167 </tr>
168 <tr>
169 <td style="text-align:left;">TACTAAYM</td>
170 <td style="text-align:left;">MEME-1</td>
171 <td style="text-align:left;">chrM</td>
172 <td style="text-align:center;">+</td>
173 <td style="text-align:left;">13740</td>
174 <td style="text-align:left;">13747</td>
175 <td style="text-align:left;">2.18e-05</td>
176 <td style="text-align:left;">0.142</td>
177 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
178 </tr>
179 <tr>
180 <td style="text-align:left;">TACTAAYM</td>
181 <td style="text-align:left;">MEME-1</td>
182 <td style="text-align:left;">chrM</td>
183 <td style="text-align:center;">+</td>
184 <td style="text-align:left;">861</td>
185 <td style="text-align:left;">868</td>
186 <td style="text-align:left;">3.96e-05</td>
187 <td style="text-align:left;">0.185</td>
188 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACC</td>
189 </tr>
190 <tr>
191 <td style="text-align:left;">TACTAAYM</td>
192 <td style="text-align:left;">MEME-1</td>
193 <td style="text-align:left;">chrM</td>
194 <td style="text-align:center;">+</td>
195 <td style="text-align:left;">9346</td>
196 <td style="text-align:left;">9353</td>
197 <td style="text-align:left;">3.96e-05</td>
198 <td style="text-align:left;">0.185</td>
199 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACC</td>
200 </tr>
201 <tr>
202 <td style="text-align:left;">TACTAAYM</td>
203 <td style="text-align:left;">MEME-1</td>
204 <td style="text-align:left;">chrM</td>
205 <td style="text-align:center;">+</td>
206 <td style="text-align:left;">3767</td>
207 <td style="text-align:left;">3774</td>
208 <td style="text-align:left;">6.62e-05</td>
209 <td style="text-align:left;">0.216</td>
210 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td>
211 </tr>
212 <tr>
213 <td style="text-align:left;">TACTAAYM</td>
214 <td style="text-align:left;">MEME-1</td>
215 <td style="text-align:left;">chrM</td>
216 <td style="text-align:center;">+</td>
217 <td style="text-align:left;">5497</td>
218 <td style="text-align:left;">5504</td>
219 <td style="text-align:left;">6.62e-05</td>
220 <td style="text-align:left;">0.216</td>
221 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td>
222 </tr>
223 <tr>
224 <td style="text-align:left;">TACTAAYM</td>
225 <td style="text-align:left;">MEME-1</td>
226 <td style="text-align:left;">chrM</td>
227 <td style="text-align:center;">+</td>
228 <td style="text-align:left;">10105</td>
229 <td style="text-align:left;">10112</td>
230 <td style="text-align:left;">6.62e-05</td>
231 <td style="text-align:left;">0.216</td>
232 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td>
233 </tr>
234 <tr>
235 <td style="text-align:left;">TACTAAYM</td>
236 <td style="text-align:left;">MEME-1</td>
237 <td style="text-align:left;">chrM</td>
238 <td style="text-align:center;">+</td>
239 <td style="text-align:left;">10959</td>
240 <td style="text-align:left;">10966</td>
241 <td style="text-align:left;">8.79e-05</td>
242 <td style="text-align:left;">0.261</td>
243 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACT</td>
244 </tr>
245 </tbody>
246 </table>
247
248 <hr>
249 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
250 <hr>
251 <p>
252 Command line:
253 </p>
254 <pre>
255 fimo -oc fimo_test1_out meme_fimo_input_1.xml hsa_chrM.fa
256 </pre>
257 <p>
258 Settings:
259 </p>
260 <pre>
261 <table>
262 <tr>
263 <td style="padding-right: 2em">output_directory = fimo_test1_out</td>
264 <td style="padding-left: 5em; padding-right: 2em">MEME file name = meme_fimo_input_1.xml</td>
265 <td style="padding-left: 5em; padding-right: 2em">sequence file name = hsa_chrM.fa</td>
266 </tr> <tr>
267 <td style="padding-right: 2em">background file name = --nrdb--</td>
268 <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>
269 <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>
270 </tr> <tr>
271 <td style="padding-right: 2em">allow clobber = true</td>
272 <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
273 <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>
274 </tr>
275 <tr>
276 <td style="padding-right: 2em">text only = false</td>
277 <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
278 <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
279 </tr>
280 <tr>
281 <td style="padding-right: 2em">threshold type = p-value</td>
282 <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>
283 <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
284 </tr>
285 <tr>
286 <td style="padding-right: 2em">alpha = 1</td>
287 <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
288 <td style="padding-left: 5em; padding-right: 2em"></td>
289 </tr>
290
291 </table>
292 </pre>
293 <p>
294 This information can be useful in the event you wish to report a
295 problem with the FIMO software.
296 </p>
297 <hr>
298 <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
299 </body>
300 </html>