Mercurial > repos > iuc > meme_fimo
comparison test-data/fimo_output_test1.html @ 15:0c5239d1aa65 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
author | iuc |
---|---|
date | Wed, 11 Dec 2019 18:05:35 -0500 |
parents | 4eb02864e5df |
children | c5209f38700d |
comparison
equal
deleted
inserted
replaced
14:c1a9a297ba8b | 15:0c5239d1aa65 |
---|---|
5 <meta charset="UTF-8"> | 5 <meta charset="UTF-8"> |
6 <title>FIMO Results</title> | 6 <title>FIMO Results</title> |
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> | |
11 </head> | 10 </head> |
12 <body bgcolor="#D5F0FF"> | 11 <body color="#000000"> |
13 <a name="top_buttons"></a> | 12 <a name="top_buttons"></a> |
14 <hr> | 13 <hr> |
15 <table summary="buttons" align="left" cellspacing="0"> | 14 <table summary="buttons" align="left" cellspacing="0"> |
16 <tr> | 15 <tr> |
17 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td> | 16 <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> | 17 <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> | 18 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td> |
19 <td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td> | |
20 <td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td> | |
20 </tr> | 21 </tr> |
21 </table> | 22 </table> |
22 <br/> | |
23 <br/> | |
24 <hr/> | |
25 <center><big><b>FIMO - Motif search tool</b></big></center> | 23 <center><big><b>FIMO - Motif search tool</b></big></center> |
26 <hr> | 24 FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700) |
27 <p> | 25 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) | 26 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> | 27 <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, | 28 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, |
36 "FIMO: Scanning for occurrences of a given motif", | 29 "FIMO: Scanning for occurrences of a given motif", |
37 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011. | 30 <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> | 31 <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 | 32 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 | 33 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--): | 34 Random model letter frequencies (--nrdb--): |
71 <br/> | |
72 | |
73 A 0.275 C 0.225 G 0.225 T 0.275 </p> | 35 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> | 36 <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. | 37 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 | 38 The full set of motif occurences can be seen in the |
83 tab-delimited plain text output file | 39 TSV (tab-delimited values) output file |
84 <a href="fimo.txt">fimo.txt</a>, | 40 The <i>p</i>-value of a motif occurrence is defined as the |
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 | 41 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. | 42 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 | 43 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 | 44 is computed by summing the appropriate entries from each column of |
101 the position-dependent scoring matrix that represents the motif. | 45 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 | 46 The q-value of a motif occurrence is defined as the |
105 false discovery rate if the occurrence is accepted as significant. | 47 false discovery rate if the occurrence is accepted as significant. |
106 </li> | 48 <li>The table is sorted by increasing <i>p</i>-value.</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> | 49 <th>Motif ID</th> |
113 <th>Alt ID</th> | 50 <th>Alt ID</th> |
114 <th>Sequence Name</th> | 51 <th>Sequence Name</th> |
115 <th>Strand</th> | 52 <th>Strand</th> |
116 <th>Start</th> | 53 <th>Start</th> |
117 <th>End</th> | 54 <th>End</th> |
118 <th>p-value</th> | 55 <th>p-value</th> |
119 <th>q-value</th> | 56 <th>q-value</th> |
120 <th>Matched Sequence</th> | 57 <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> | 58 <td style="text-align:left;">TACTAAYM</td> |
137 <td style="text-align:left;">MEME-1</td> | 59 <td style="text-align:left;">MEME-1</td> |
138 <td style="text-align:left;">chrM</td> | 60 <td style="text-align:left;">chrM</td> |
139 <td style="text-align:center;">+</td> | 61 <td style="text-align:center;">+</td> |
140 <td style="text-align:left;">6529</td> | 62 <td style="text-align:left;">6529</td> |
141 <td style="text-align:left;">6536</td> | 63 <td style="text-align:left;">6536</td> |
142 <td style="text-align:left;">2.18e-05</td> | 64 <td style="text-align:left;">2.18e-05</td> |
143 <td style="text-align:left;">0.142</td> | 65 <td style="text-align:left;">0.142</td> |
144 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td> | 66 <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> | 67 </table> |
247 | |
248 <hr> | 68 <hr> |
249 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center> | 69 <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 | 70 This information can be useful in the event you wish to report a |
295 problem with the FIMO software. | 71 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> | 72 </body> |
300 </html> | 73 </html> |