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comparison test-data/fimo_output_test2.html @ 18:c5209f38700d draft

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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 08:32:23 +0000
parents 0c5239d1aa65
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17:d7a6ea1e3b9d 18:c5209f38700d
1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> 1 <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</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">max stored scores = 100000</td>
3 <head> 3 </tr> <tr>
4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> 4 <td style="padding-right: 2em">allow clobber = false</td>
5 <meta charset="UTF-8"> 5 <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
6 <title>FIMO Results</title> 6 <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>
7 <style type="text/css"> 7 </tr>
8 td.left {text-align: left;} 8 <tr>
9 td.right {text-align: right; padding-right: 1cm;} 9 <td style="padding-right: 2em">text only = false</td>
10 </style> 10 <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
11 </head> 11 <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
12 <body color="#000000"> 12 </tr>
13 <a name="top_buttons"></a> 13 <tr>
14 <hr> 14 <td style="padding-right: 2em">threshold type = p-value</td>
15 <table summary="buttons" align="left" cellspacing="0"> 15 <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>
16 <tr> 16 <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
17 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td> 17 </tr>
18 <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td> 18 <tr>
19 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td> 19 <td style="padding-right: 2em">alpha = 1</td>
20 <td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td> 20 <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
21 <td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td> 21 <td style="padding-left: 5em; padding-right: 2em"></td>
22 </tr> 22 </tr>
23
23 </table> 24 </table>
24 <center><big><b>FIMO - Motif search tool</b></big></center> 25 </pre>
25 FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700) 26 <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>
27 To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>
28 <p>If you use FIMO in your research, please cite the following paper:<br>
29 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
30 "FIMO: Scanning for occurrences of a given motif",
31 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
32 <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
33 Database contains 1 sequences, 16569 residues
34 <table>
35 <thead>
36 </thead>
37 <tbody>
38 </tbody>
39 </table>
40 A 0.278 C 0.222 G 0.222 T 0.278 </p>
41 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
42 There were 11 motif occurences with a p-value less than 0.0001.
43 The full set of motif occurences can be seen in the
44 TSV (tab-delimited values) output file
45 the GFF3 file
46 which may be suitable for uploading to the
47 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
48 or the XML file
49 The <i>p</i>-value of a motif occurrence is defined as the
50 probability of a random sequence of the same length as the motif
51 matching that position of the sequence with as good or better a score.
52 The score for the match of a position in a sequence to a motif
53 is computed by summing the appropriate entries from each column of
54 the position-dependent scoring matrix that represents the motif.
55 The q-value of a motif occurrence is defined as the
56 false discovery rate if the occurrence is accepted as significant.
57 <li>The table is sorted by increasing <i>p</i>-value.</li>
58 <th>Motif ID</th>
59 <th>Alt ID</th>
60 <th>Sequence Name</th>
61 <th>Strand</th>
62 <th>Start</th>
63 <th>End</th>
64 <th>p-value</th>
65 <th>q-value</th>
66 <th>Matched Sequence</th>
67 <tr>
68 <td style="text-align:left;">CCAGCAY</td>
69 <td style="text-align:left;">DREME-5</td>
70 <td style="text-align:left;">chrM</td>
71 <td style="text-align:center;">+</td>
72 <td style="text-align:left;">510</td>
73 <td style="text-align:left;">516</td>
74 <td style="text-align:left;">4.15e-05</td>
75 <td style="text-align:left;">0.683</td>
76 <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
77 <td style="text-align:left;">2093</td>
78 <td style="text-align:left;">2099</td>
79 <td style="text-align:left;">8.2e-05</td>
80 <td style="text-align:left;">0.332</td>
81 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
82 </tr>
83 <hr>
84 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
85 Command line:
86 Settings:
87 This information can be useful in the event you wish to report a 27 This information can be useful in the event you wish to report a
88 problem with the FIMO software. 28 problem with the FIMO software.
29 </p>
30 <hr>
31 <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
89 </body> 32 </body>
90 </html> 33 </html>