Mercurial > repos > iuc > meme_fimo
comparison test-data/fimo_output_test3.html @ 18:c5209f38700d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
author | iuc |
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date | Sat, 09 Apr 2022 08:32:23 +0000 |
parents | 0c5239d1aa65 |
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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> |