Mercurial > repos > iuc > meme_fimo

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<title>FIMO Results</title>
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<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>
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<center><big><b>FIMO - Motif search tool</b></big></center>
<hr>
<p>
FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)
</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 hsa_chrM.fa
  <br />
  Database contains 1 sequences, 16569 residues
</p>
<p>
  MOTIFS meme_fimo_input_1.xml (DNA)
  <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;">TACTAAYM</td>
        <td style="text-align:right;padding-left: 1em;">8</td>
        <td style="text-align:left;padding-left: 1em;">TACTAACA</td>
       </tr>
    </tbody>
  </table>
</p>
<p>
Random model letter frequencies (--nrdb--):
<br/>

A 0.275 C 0.225 G 0.225 T 0.275 </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 11 motif occurences with a p-value less than 0.0001.

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>
<li>
The score for the match of a position in a sequence to a motif
is computed by summing the appropriate entries from each column of
the position-dependent scoring matrix that represents the motif.
</li>
<li>
The q-value of a motif occurrence is defined as the
false discovery rate if the occurrence is accepted as significant.
</li>
<li>The table is sorted by increasing p-value.</li>
</ul>
<table border="1">
<thead>
<tr>
<th>Motif ID</th>
<th>Alt ID</th>
<th>Sequence Name</th>
<th>Strand</th>
<th>Start</th>
<th>End</th>
<th>p-value</th>
<th>q-value</th>
<th>Matched Sequence</th>
</tr>
</thead>
<tbody>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">-</td>
      <td style="text-align:left;">2299</td>
      <td style="text-align:left;">2306</td>
      <td style="text-align:left;">2.18e-05</td>
      <td style="text-align:left;">0.142</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">6529</td>
      <td style="text-align:left;">6536</td>
      <td style="text-align:left;">2.18e-05</td>
      <td style="text-align:left;">0.142</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">7741</td>
      <td style="text-align:left;">7748</td>
      <td style="text-align:left;">2.18e-05</td>
      <td style="text-align:left;">0.142</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">13656</td>
      <td style="text-align:left;">13663</td>
      <td style="text-align:left;">2.18e-05</td>
      <td style="text-align:left;">0.142</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">13740</td>
      <td style="text-align:left;">13747</td>
      <td style="text-align:left;">2.18e-05</td>
      <td style="text-align:left;">0.142</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">861</td>
      <td style="text-align:left;">868</td>
      <td style="text-align:left;">3.96e-05</td>
      <td style="text-align:left;">0.185</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACC</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">9346</td>
      <td style="text-align:left;">9353</td>
      <td style="text-align:left;">3.96e-05</td>
      <td style="text-align:left;">0.185</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACC</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">3767</td>
      <td style="text-align:left;">3774</td>
      <td style="text-align:left;">6.62e-05</td>
      <td style="text-align:left;">0.216</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">5497</td>
      <td style="text-align:left;">5504</td>
      <td style="text-align:left;">6.62e-05</td>
      <td style="text-align:left;">0.216</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">10105</td>
      <td style="text-align:left;">10112</td>
      <td style="text-align:left;">6.62e-05</td>
      <td style="text-align:left;">0.216</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td>
   </tr>
    <tr>
      <td style="text-align:left;">TACTAAYM</td>
      <td style="text-align:left;">MEME-1</td>
      <td style="text-align:left;">chrM</td>
      <td style="text-align:center;">+</td>
      <td style="text-align:left;">10959</td>
      <td style="text-align:left;">10966</td>
      <td style="text-align:left;">8.79e-05</td>
      <td style="text-align:left;">0.261</td>
      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACT</td>
   </tr>
</tbody>
</table>

<hr>
<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
<hr>
<p>
Command line:
</p>
<pre>
fimo -oc fimo_test1_out meme_fimo_input_1.xml hsa_chrM.fa
</pre>
<p>
Settings:
</p>
<pre>
<table>
  <tr>
    <td style="padding-right: 2em">output_directory = fimo_test1_out</td>
    <td style="padding-left: 5em; padding-right: 2em">MEME file name = meme_fimo_input_1.xml</td>
    <td style="padding-left: 5em; padding-right: 2em">sequence file name = hsa_chrM.fa</td>
  </tr>  <tr>
    <td style="padding-right: 2em">background file name = --nrdb--</td>
    <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>
    <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>
  </tr>  <tr>
    <td style="padding-right: 2em">allow clobber = true</td>
    <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
    <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>
  </tr>
  <tr>
    <td style="padding-right: 2em">text only = false</td>
    <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
    <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
  </tr>
  <tr>
    <td style="padding-right: 2em">threshold type = p-value</td>
    <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>
    <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
  </tr>
  <tr>
    <td style="padding-right: 2em">alpha = 1</td>
    <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
    <td style="padding-left: 5em; padding-right: 2em"></td>
  </tr>

</table>
</pre>
<p>
This information can be useful in the event you wish to report a
problem with the FIMO software.
</p>
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author	iuc
date	Thu, 17 May 2018 14:11:00 -0400
parents
children	0c5239d1aa65