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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 08:33:29 +0000
parents ff2f53a32d0e
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5:164067a66a5c 6:5f95d385a33c
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 = --uniform--</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 </head> 8 </tr>
9 <body color="#000000"> 9 <tr>
10 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td> 10 <td style="padding-right: 2em">text only = false</td>
11 <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td> 11 <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
12 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td> 12 <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
13 <td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td> 13 </tr>
14 <td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td> 14 <tr>
15 <center><big><b>FIMO - Motif search tool</b></big></center> 15 <td style="padding-right: 2em">threshold type = p-value</td>
16 FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700) 16 <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.01</td>
17 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> 17 <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
18 To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a> 18 </tr>
19 <p>If you use FIMO in your research, please cite the following paper:<br> 19 <tr>
20 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, 20 <td style="padding-right: 2em">alpha = 1</td>
21 "FIMO: Scanning for occurrences of a given motif", 21 <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
22 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011. 22 <td style="padding-left: 5em; padding-right: 2em"></td>
23 <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center> 23 </tr>
24 Database contains 1 sequences, 16569 residues
25 <table>
26 <thead>
27 <tr>
28 <th style="border-bottom: 1px dashed;">MOTIF</th>
29 <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
30 <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >
31 BEST POSSIBLE MATCH
32 </th>
33 </tr>
34 </thead>
35 <tbody>
36 <tr>
37 <td style="text-align:right;">ACTAAYH</td>
38 <td style="text-align:right;padding-left: 1em;">7</td>
39 <td style="text-align:left;padding-left: 1em;">ACTAACA</td>
40 </tr>
41 </tbody>
42 </table>
43 </p>
44 <p>
45 Random model letter frequencies (--uniform--):
46 A 0.250 C 0.250 G 0.250 T 0.250 </p>
47 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
48 There were 517 motif occurences with a p-value less than 0.01.
49 The full set of motif occurences can be seen in the
50 TSV (tab-delimited values) output file
51 the GFF3 file
52 which may be suitable for uploading to the
53 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
54 or the XML file
55 The <i>p</i>-value of a motif occurrence is defined as the
56 probability of a random sequence of the same length as the motif
57 matching that position of the sequence with as good or better a score.
58 The score for the match of a position in a sequence to a motif
59 is computed by summing the appropriate entries from each column of
60 the position-dependent scoring matrix that represents the motif.
61 The q-value of a motif occurrence is defined as the
62 false discovery rate if the occurrence is accepted as significant.
63 <li>The table is sorted by increasing <i>p</i>-value.</li>
64 <table border="1">
65 <thead>
66 <tr>
67 <th>Motif ID</th>
68 <th>Alt ID</th>
69 <th>Sequence Name</th>
70 <th>Strand</th>
71 <th>Start</th>
72 <th>End</th>
73 <th>p-value</th>
74 <th>q-value</th>
75 <th>Matched Sequence</th>
76 </tr>
77 </thead>
78 <tbody>
79 <tr>
80 <td style="text-align:left;">ACTAAYH</td>
81 <td style="text-align:left;">DREME-1</td>
82 <td style="text-align:left;">chrM</td>
83 <td style="text-align:center;">+</td>
84 <td style="text-align:left;">440</td>
85 <td style="text-align:left;">446</td>
86 <td style="text-align:left;">6.1e-05</td>
87 <td style="text-align:left;">0.239</td>
88 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
89 This information can be useful in the event you wish to report a
90 problem with the FIMO software.
91 </body>
92 </html>