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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit ef11594cf3ca79e444ab4e30d83de5951a636faf
author iuc
date Sun, 10 Jul 2016 09:02:25 -0400
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6:62d1fae3b7d3 7:487ce3fa1822
1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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">
3 <head>
4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
5 <meta charset="UTF-8">
6 <title>FIMO Results</title>
7 <style type="text/css">
8 td.left {text-align: left;}
9 td.right {text-align: right; padding-right: 1cm;}
10 </style>
11 </head>
12 <body bgcolor="#D5F0FF">
13 <a name="top_buttons"></a>
14 <hr>
15 <table summary="buttons" align="left" cellspacing="0">
16 <tr>
17 <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>
19 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
20 </tr>
21 </table>
22 <br/>
23 <br/>
24 <hr/>
25 <center><big><b>FIMO - Motif search tool</b></big></center>
26 <hr>
27 <p>
28 FIMO version 4.11.1, (Release date: Fri Jan 15 12:51:59 2016 -0800)
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>
35 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
36 "FIMO: Scanning for occurrences of a given motif",
37 <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>
41 <hr>
42 <div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
43 <p>
44 <br />
45 Database contains 1 sequences, 5386 residues
46 </p>
47 <p>
48 <table>
49 <thead>
50 <tr>
51 <th style="border-bottom: 1px dashed;">MOTIF</th>
52 <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
53 <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >
54 BEST POSSIBLE MATCH
55 </th>
56 </tr>
57 </thead>
58 <tbody>
59 <tr>
60 <td style="text-align:right;">1</td>
61 <td style="text-align:right;padding-left: 1em;">11</td>
62 <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td>
63 </tr>
64 </tbody>
65 </table>
66 </p>
67 <p>
68 Random model letter frequencies (from non-redundant database):
69 <br/>
70
71 A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058
72 L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064
73 W 0.013 Y 0.033 </p>
74 </div>
75 <hr>
76 <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 1937 motif occurences with a p-value less than 0.0001.
81 <b>Only the most significant 1000 matches are shown here.</b>
82
83 The full set of motif occurences can be seen in the
84 tab-delimited plain text output file
85 <a href="fimo.txt">fimo.txt</a>,
86 the GFF file
87 <a href="fimo.gff">fimo.gff</a>
88 which may be suitable for uploading to the
89 <a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
90 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
91 or the XML file
92 <a href="fimo.xml">fimo.xml</a>.
93 </li>
94 <li>
95 The p-value of a motif occurrence is defined as the
96 probability of a random sequence of the same length as the motif
97 matching that position of the sequence with as good or better a score.
98 </li>
99 <li>
100 The score for the match of a position in a sequence to a motif