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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
author iuc
date Sat, 09 Apr 2022 08:34:02 +0000
parents 3f0dd362b755
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17:e7242484929c 18:19237efe98d1
1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> 1 <td style="padding-right: 2em">background file name = --nrdb--</td>
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"> 2 <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>
3 <head> 3 <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>
4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> 4 </tr> <tr>
5 <meta charset="UTF-8"> 5 <td style="padding-right: 2em">allow clobber = false</td>
6 <title>FIMO Results</title> 6 <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
7 <style type="text/css"> 7 <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>
8 td.left {text-align: left;} 8 </tr>
9 td.right {text-align: right; padding-right: 1cm;} 9 <tr>
10 </head> 10 <td style="padding-right: 2em">text only = false</td>
11 <body color="#000000"> 11 <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
12 <a name="top_buttons"></a> 12 <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
13 <hr> 13 </tr>
14 <table summary="buttons" align="left" cellspacing="0"> 14 <tr>
15 <tr> 15 <td style="padding-right: 2em">threshold type = p-value</td>
16 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td> 16 <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>
17 <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td> 17 <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
18 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td> 18 </tr>
19 <td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td> 19 <tr>
20 <td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td> 20 <td style="padding-right: 2em">alpha = 1</td>
21 </tr> 21 <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
22 <td style="padding-left: 5em; padding-right: 2em"></td>
23 </tr>
24
22 </table> 25 </table>
23 <center><big><b>FIMO - Motif search tool</b></big></center> 26 </pre>
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>
26 To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>
27 <p>If you use FIMO in your research, please cite the following paper:<br>
28 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
29 "FIMO: Scanning for occurrences of a given motif",
30 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
31 <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
32 Database contains 1 sequences, 16569 residues
33 BEST POSSIBLE MATCH
34 Random model letter frequencies (--nrdb--):
35 A 0.275 C 0.225 G 0.225 T 0.275 </p>
36 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
37 There were 11 motif occurences with a p-value less than 0.0001.
38 The full set of motif occurences can be seen in the
39 TSV (tab-delimited values) output file
40 The <i>p</i>-value of a motif occurrence is defined as the
41 probability of a random sequence of the same length as the motif
42 matching that position of the sequence with as good or better a score.
43 The score for the match of a position in a sequence to a motif
44 is computed by summing the appropriate entries from each column of
45 the position-dependent scoring matrix that represents the motif.
46 The q-value of a motif occurrence is defined as the
47 false discovery rate if the occurrence is accepted as significant.
48 <li>The table is sorted by increasing <i>p</i>-value.</li>
49 <th>Motif ID</th>
50 <th>Alt ID</th>
51 <th>Sequence Name</th>
52 <th>Strand</th>
53 <th>Start</th>
54 <th>End</th>
55 <th>p-value</th>
56 <th>q-value</th>
57 <th>Matched Sequence</th>
58 <td style="text-align:left;">TACTAAYM</td>
59 <td style="text-align:left;">MEME-1</td>
60 <td style="text-align:left;">chrM</td>
61 <td style="text-align:center;">+</td>
62 <td style="text-align:left;">6529</td>
63 <td style="text-align:left;">6536</td>
64 <td style="text-align:left;">2.18e-05</td>
65 <td style="text-align:left;">0.142</td>
66 <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
67 </table>
68 <hr>
69 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
70 This information can be useful in the event you wish to report a 28 This information can be useful in the event you wish to report a
71 problem with the FIMO software. 29 problem with the FIMO software.
30 </p>
31 <hr>
32 <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
72 </body> 33 </body>
73 </html> 34 </html>