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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
author iuc
date Wed, 11 Dec 2019 18:04:34 -0500
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7 <style type="text/css"> 7 <style type="text/css">
8 td.left {text-align: left;} 8 td.left {text-align: left;}
9 td.right {text-align: right; padding-right: 1cm;} 9 td.right {text-align: right; padding-right: 1cm;}
10 </style> 10 </style>
11 </head> 11 </head>
12 <body bgcolor="#D5F0FF"> 12 <body color="#000000">
13 <a name="top_buttons"></a> 13 <a name="top_buttons"></a>
14 <hr> 14 <hr>
15 <table summary="buttons" align="left" cellspacing="0"> 15 <table summary="buttons" align="left" cellspacing="0">
16 <tr> 16 <tr>
17 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td> 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> 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> 19 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
20 <td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td>
21 <td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td>
20 </tr> 22 </tr>
21 </table> 23 </table>
22 <br/>
23 <br/>
24 <hr/>
25 <center><big><b>FIMO - Motif search tool</b></big></center> 24 <center><big><b>FIMO - Motif search tool</b></big></center>
26 <hr> 25 FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700)
27 <p> 26 For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br>
28 FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700) 27 To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>
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> 28 <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, 29 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
36 "FIMO: Scanning for occurrences of a given motif", 30 "FIMO: Scanning for occurrences of a given motif",
37 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011. 31 <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> 32 <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 33 Database contains 1 sequences, 16569 residues
47 </p>
48 <p>
49 MOTIFS dreme_fimo_input_1.xml (DNA)
50 <table> 34 <table>
51 <thead> 35 <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> 36 </thead>
60 <tbody> 37 <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> 38 </tbody>
92 </table> 39 </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> 40 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> 41 <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. 42 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 43 The full set of motif occurences can be seen in the
108 tab-delimited plain text output file 44 TSV (tab-delimited values) output file
109 <a href="fimo.txt">fimo.txt</a>, 45 the GFF3 file
110 the GFF file
111 <a href="fimo.gff">fimo.gff</a>
112 which may be suitable for uploading to the 46 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), 47 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
115 or the XML file 48 or the XML file
116 <a href="fimo.xml">fimo.xml</a>. 49 The <i>p</i>-value of a motif occurrence is defined as the
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 50 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. 51 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 52 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 53 is computed by summing the appropriate entries from each column of
126 the position-dependent scoring matrix that represents the motif. 54 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 55 The q-value of a motif occurrence is defined as the
130 false discovery rate if the occurrence is accepted as significant. 56 false discovery rate if the occurrence is accepted as significant.
131 </li> 57 <li>The table is sorted by increasing <i>p</i>-value.</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> 58 <th>Motif ID</th>
138 <th>Alt ID</th> 59 <th>Alt ID</th>
139 <th>Sequence Name</th> 60 <th>Sequence Name</th>
140 <th>Strand</th> 61 <th>Strand</th>
141 <th>Start</th> 62 <th>Start</th>
142 <th>End</th> 63 <th>End</th>
143 <th>p-value</th> 64 <th>p-value</th>
144 <th>q-value</th> 65 <th>q-value</th>
145 <th>Matched Sequence</th> 66 <th>Matched Sequence</th>
146 </tr>
147 </thead>
148 <tbody>
149 <tr> 67 <tr>
150 <td style="text-align:left;">CCAGCAY</td> 68 <td style="text-align:left;">CCAGCAY</td>
151 <td style="text-align:left;">DREME-5</td> 69 <td style="text-align:left;">DREME-5</td>
152 <td style="text-align:left;">chrM</td> 70 <td style="text-align:left;">chrM</td>
153 <td style="text-align:center;">+</td> 71 <td style="text-align:center;">+</td>
154 <td style="text-align:left;">510</td> 72 <td style="text-align:left;">510</td>
155 <td style="text-align:left;">516</td> 73 <td style="text-align:left;">516</td>
156 <td style="text-align:left;">4.15e-05</td> 74 <td style="text-align:left;">4.15e-05</td>
157 <td style="text-align:left;">0.668</td> 75 <td style="text-align:left;">0.683</td>
158 <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td> 76 <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> 77 <td style="text-align:left;">2093</td>
188 <td style="text-align:left;">2099</td> 78 <td style="text-align:left;">2099</td>
189 <td style="text-align:left;">8.2e-05</td> 79 <td style="text-align:left;">8.2e-05</td>
190 <td style="text-align:left;">0.327</td> 80 <td style="text-align:left;">0.332</td>
191 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td> 81 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
192 </tr> 82 </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> 83 <hr>
274 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center> 84 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
275 <hr>
276 <p>
277 Command line: 85 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: 86 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 87 This information can be useful in the event you wish to report a
320 problem with the FIMO software. 88 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>
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