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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 17:02:11 -0500
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<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">
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<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="UTF-8">
<title>FIMO Results</title>
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td.right {text-align: right; padding-right: 1cm;}
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<body bgcolor="#D5F0FF">
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<tr>
<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
</tr>
</table>
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<br/>
<hr/>
<center><big><b>FIMO - Motif search tool</b></big></center>
<hr>
<p>
FIMO version 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000)
</p>
<p>
For further information on how to interpret these results
or to get a copy of the FIMO software please access
<a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>
<p>If you use FIMO in your research, please cite the following paper:<br>
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
"FIMO: Scanning for occurrences of a given motif",
<i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
<a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p>
<hr>
<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
<hr>
<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
<p>
  DATABASE /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat
  <br />
  Database contains 1 sequences, 5386 residues
</p>
<p>
  MOTIFS /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat (Protein)
  <table>
    <thead>
      <tr>
        <th style="border-bottom: 1px dashed;">MOTIF</th>
        <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
        <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >
         BEST POSSIBLE MATCH
        </th>
      </tr>
    </thead>
    <tbody>
      <tr>
        <td style="text-align:right;">1</td>
        <td style="text-align:right;padding-left: 1em;">11</td>
        <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td>
       </tr>
    </tbody>
  </table>
</p>
<p>
Random model letter frequencies (from non-redundant database):
<br/>

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 
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 
W 0.013 Y 0.033 </p>
</div>
<hr>
<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
<hr>
<ul>
<li>
There were 1937 motif occurences with a p-value less than 0.0001.
<b>Only the most significant 1000 matches are shown here.</b>

The full set of motif occurences can be seen in the
tab-delimited plain text output file
<a href="fimo.txt">fimo.txt</a>, 
the GFF file 
<a href="fimo.gff">fimo.gff</a> 
which may be suitable for uploading to the 
<a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
or the XML file 
<a href="fimo.xml">fimo.xml</a>.
</li>
<li>
The p-value of a motif occurrence is defined as the
probability of a random sequence of the same length as the motif
matching that position of the sequence with as good or better a score.
</li>