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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
author iuc
date Tue, 22 Dec 2015 17:01:51 -0500
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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 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000)
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 DATABASE /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat
45 <br />
46 Database contains 1 sequences, 5386 residues
47 </p>
48 <p>
49 MOTIFS /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat (Protein)
50 <table>
51 <thead>
52 <tr>
53 <th style="border-bottom: 1px dashed;">MOTIF</th>
54 <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
55 <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >
56 BEST POSSIBLE MATCH
57 </th>
58 </tr>
59 </thead>
60 <tbody>
61 <tr>
62 <td style="text-align:right;">1</td>
63 <td style="text-align:right;padding-left: 1em;">11</td>
64 <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td>
65 </tr>
66 </tbody>
67 </table>
68 </p>
69 <p>
70 Random model letter frequencies (from non-redundant database):
71 <br/>
72
73 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
74 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
75 W 0.013 Y 0.033 </p>
76 </div>
77 <hr>
78 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
79 <hr>
80 <ul>
81 <li>
82 There were 1937 motif occurences with a p-value less than 0.0001.
83 <b>Only the most significant 1000 matches are shown here.</b>
84
85 The full set of motif occurences can be seen in the
86 tab-delimited plain text output file
87 <a href="fimo.txt">fimo.txt</a>,
88 the GFF file
89 <a href="fimo.gff">fimo.gff</a>
90 which may be suitable for uploading to the
91 <a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
92 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
93 or the XML file
94 <a href="fimo.xml">fimo.xml</a>.
95 </li>
96 <li>
97 The p-value of a motif occurrence is defined as the
98 probability of a random sequence of the same length as the motif
99 matching that position of the sequence with as good or better a score.
100 </li>