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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 dreme_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;">ACTAAYH</td>
63 <td style="text-align:right;padding-left: 1em;">7</td>
64 <td style="text-align:left;padding-left: 1em;">ACTAACA</td>
65 </tr>
66 <tr>
67 <td style="text-align:right;">YTAACA</td>
68 <td style="text-align:right;padding-left: 1em;">6</td>
69 <td style="text-align:left;padding-left: 1em;">TTAACA</td>
70 </tr>
71 <tr>
72 <td style="text-align:right;">TCTGT</td>
73 <td style="text-align:right;padding-left: 1em;">5</td>
74 <td style="text-align:left;padding-left: 1em;">TCTGT</td>
75 </tr>
76 <tr>
77 <td style="text-align:right;">SCCAGG</td>
78 <td style="text-align:right;padding-left: 1em;">6</td>
79 <td style="text-align:left;padding-left: 1em;">CCCAGG</td>
80 </tr>
81 <tr>
82 <td style="text-align:right;">CCAGCAY</td>
83 <td style="text-align:right;padding-left: 1em;">7</td>
84 <td style="text-align:left;padding-left: 1em;">CCAGCAC</td>
85 </tr>
86 <tr>
87 <td style="text-align:right;">GMATGT</td>
88 <td style="text-align:right;padding-left: 1em;">6</td>
89 <td style="text-align:left;padding-left: 1em;">GAATGT</td>
90 </tr>
91 </tbody>
92 </table>
93 </p>
94 <p>
95 Random model letter frequencies (fimo_background_probs_hsa_chrM.txt):
96 <br/>
97
98 A 0.278 C 0.222 G 0.222 T 0.278 </p>
99 </div>
100 <hr>
101 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
102 <hr>
103 <ul>
104 <li>
105 There were 11 motif occurences with a p-value less than 0.0001.
106
107 The full set of motif occurences can be seen in the
108 tab-delimited plain text output file
109 <a href="fimo.txt">fimo.txt</a>,
110 the GFF file
111 <a href="fimo.gff">fimo.gff</a>
112 which may be suitable for uploading to the
113 <a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
114 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
115 or the XML file
116 <a href="fimo.xml">fimo.xml</a>.
117 </li>
118 <li>
119 The p-value of a motif occurrence is defined as the
120 probability of a random sequence of the same length as the motif
121 matching that position of the sequence with as good or better a score.
122 </li>
123 <li>
124 The score for the match of a position in a sequence to a motif
125 is computed by summing the appropriate entries from each column of
126 the position-dependent scoring matrix that represents the motif.
127 </li>
128 <li>
129 The q-value of a motif occurrence is defined as the
130 false discovery rate if the occurrence is accepted as significant.
131 </li>
132 <li>The table is sorted by increasing p-value.</li>
133 </ul>
134 <table border="1">
135 <thead>
136 <tr>
137 <th>Motif ID</th>
138 <th>Alt ID</th>
139 <th>Sequence Name</th>
140 <th>Strand</th>
141 <th>Start</th>
142 <th>End</th>
143 <th>p-value</th>
144 <th>q-value</th>
145 <th>Matched Sequence</th>
146 </tr>
147 </thead>
148 <tbody>
149 <tr>
150 <td style="text-align:left;">CCAGCAY</td>
151 <td style="text-align:left;">DREME-5</td>
152 <td style="text-align:left;">chrM</td>
153 <td style="text-align:center;">+</td>
154 <td style="text-align:left;">510</td>
155 <td style="text-align:left;">516</td>
156 <td style="text-align:left;">4.15e-05</td>
157 <td style="text-align:left;">0.668</td>
158 <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
159 </tr>
160 <tr>
161 <td style="text-align:left;">CCAGCAY</td>
162 <td style="text-align:left;">DREME-5</td>
163 <td style="text-align:left;">chrM</td>
164 <td style="text-align:center;">+</td>
165 <td style="text-align:left;">5137</td>
166 <td style="text-align:left;">5143</td>
167 <td style="text-align:left;">4.15e-05</td>
168 <td style="text-align:left;">0.668</td>
169 <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
170 </tr>
171 <tr>
172 <td style="text-align:left;">ACTAAYH</td>
173 <td style="text-align:left;">DREME-1</td>
174 <td style="text-align:left;">chrM</td>
175 <td style="text-align:center;">+</td>
176 <td style="text-align:left;">440</td>
177 <td style="text-align:left;">446</td>
178 <td style="text-align:left;">8.2e-05</td>
179 <td style="text-align:left;">0.327</td>
180 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
181 </tr>
182 <tr>
183 <td style="text-align:left;">ACTAAYH</td>
184 <td style="text-align:left;">DREME-1</td>
185 <td style="text-align:left;">chrM</td>
186 <td style="text-align:center;">-</td>
187 <td style="text-align:left;">2093</td>
188 <td style="text-align:left;">2099</td>
189 <td style="text-align:left;">8.2e-05</td>
190 <td style="text-align:left;">0.327</td>
191 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
192 </tr>
193 <tr>
194 <td style="text-align:left;">ACTAAYH</td>
195 <td style="text-align:left;">DREME-1</td>
196 <td style="text-align:left;">chrM</td>
197 <td style="text-align:center;">-</td>
198 <td style="text-align:left;">2299</td>
199 <td style="text-align:left;">2305</td>
200 <td style="text-align:left;">8.2e-05</td>
201 <td style="text-align:left;">0.327</td>
202 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
203 </tr>
204 <tr>
205 <td style="text-align:left;">ACTAAYH</td>
206 <td style="text-align:left;">DREME-1</td>
207 <td style="text-align:left;">chrM</td>
208 <td style="text-align:center;">+</td>
209 <td style="text-align:left;">5186</td>
210 <td style="text-align:left;">5192</td>
211 <td style="text-align:left;">8.2e-05</td>
212 <td style="text-align:left;">0.327</td>
213 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
214 </tr>
215 <tr>
216 <td style="text-align:left;">ACTAAYH</td>
217 <td style="text-align:left;">DREME-1</td>
218 <td style="text-align:left;">chrM</td>
219 <td style="text-align:center;">+</td>
220 <td style="text-align:left;">6530</td>
221 <td style="text-align:left;">6536</td>
222 <td style="text-align:left;">8.2e-05</td>
223 <td style="text-align:left;">0.327</td>
224 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
225 </tr>
226 <tr>
227 <td style="text-align:left;">ACTAAYH</td>
228 <td style="text-align:left;">DREME-1</td>
229 <td style="text-align:left;">chrM</td>
230 <td style="text-align:center;">+</td>
231 <td style="text-align:left;">7742</td>
232 <td style="text-align:left;">7748</td>
233 <td style="text-align:left;">8.2e-05</td>
234 <td style="text-align:left;">0.327</td>
235 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
236 </tr>
237 <tr>
238 <td style="text-align:left;">ACTAAYH</td>
239 <td style="text-align:left;">DREME-1</td>
240 <td style="text-align:left;">chrM</td>
241 <td style="text-align:center;">+</td>
242 <td style="text-align:left;">13657</td>
243 <td style="text-align:left;">13663</td>
244 <td style="text-align:left;">8.2e-05</td>
245 <td style="text-align:left;">0.327</td>
246 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
247 </tr>
248 <tr>
249 <td style="text-align:left;">ACTAAYH</td>
250 <td style="text-align:left;">DREME-1</td>
251 <td style="text-align:left;">chrM</td>
252 <td style="text-align:center;">+</td>
253 <td style="text-align:left;">13741</td>
254 <td style="text-align:left;">13747</td>
255 <td style="text-align:left;">8.2e-05</td>
256 <td style="text-align:left;">0.327</td>
257 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
258 </tr>
259 <tr>
260 <td style="text-align:left;">CCAGCAY</td>
261 <td style="text-align:left;">DREME-5</td>
262 <td style="text-align:left;">chrM</td>
263 <td style="text-align:center;">+</td>
264 <td style="text-align:left;">4241</td>
265 <td style="text-align:left;">4247</td>
266 <td style="text-align:left;">9.37e-05</td>
267 <td style="text-align:left;">1</td>
268 <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAT</td>
269 </tr>
270 </tbody>
271 </table>
272
273 <hr>
274 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
275 <hr>
276 <p>
277 Command line:
278 </p>
279 <pre>
280 fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa
281 </pre>
282 <p>
283 Settings:
284 </p>
285 <pre>
286 <table>
287 <tr>
288 <td style="padding-right: 2em">output_directory = fimo_test2_out</td>
289 <td style="padding-left: 5em; padding-right: 2em">MEME file name = dreme_fimo_input_1.xml</td>
290 <td style="padding-left: 5em; padding-right: 2em">sequence file name = hsa_chrM.fa</td>
291 </tr> <tr>
292 <td style="padding-right: 2em">background file name = fimo_background_probs_hsa_chrM.txt</td>
293 <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>
294 <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>
295 </tr> <tr>
296 <td style="padding-right: 2em">allow clobber = true</td>
297 <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
298 <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>
299 </tr>
300 <tr>
301 <td style="padding-right: 2em">text only = false</td>
302 <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
303 <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
304 </tr>
305 <tr>
306 <td style="padding-right: 2em">threshold type = p-value</td>
307 <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>
308 <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
309 </tr>
310 <tr>
311 <td style="padding-right: 2em">alpha = 1</td>
312 <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
313 <td style="padding-left: 5em; padding-right: 2em"></td>
314 </tr>
315
316 </table>
317 </pre>
318 <p>
319 This information can be useful in the event you wish to report a
320 problem with the FIMO software.
321 </p>
322 <hr>
323 <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
324 </body>
325 </html>