Mercurial > repos > xuebing > sharplabtool

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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>
</tr></table>
<br><br><hr>
<center><big><b>FIMO - Motif search tool</b></big></center>
<hr>
<p>
      FIMO version 4.7.0,
      (Release date: 0 EST 20)
    </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.
    </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/xuebing/Downloads/hotair-target.fa.fasta<br>
        Database contains
        832
        sequences,
        573269
        residues
      </p>
<p>
        MOTIFS
        AATAAA.motif
        (nucleotide)
        <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;" align="left">
              BEST POSSIBLE MATCH
            </th>
</tr></thead>
<tbody>
<tr>
<td align="right">AATAAA</td>
<td align="right" style="padding-left: 1em;">6</td>
<td align="left" style="padding-left: 1em;">AATAAA</td>
</tr>
<tr>
<td align="right">AATAAA</td>
<td align="right" style="padding-left: 1em;">6</td>
<td align="left" style="padding-left: 1em;">TTTATT</td>
</tr>
</tbody>
</table></p>
<p>
        Random model letter frequencies
        (from non-redundant database):
        <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> Each of the following
    0
    motif occurrences has

        p-value less than
        0.0001</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 table is sorted by increasing p-value.</li>
<li>If the start position is larger than the end position,
    the motif occurrence is on the reverse strand.
    </li>
</ul>
<table border="1">
<thead><tr>
<th>Motif</th>
<th>Sequence Name</th>
<th>Strand</th>
<th>Start</th>
<th>End</th>
<th>p-value</th>
<th>Matched Sequence</th>
</tr></thead>
<tbody></tbody>
</table>
<hr>
<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
<hr>
<p>
    Command line:
    </p>
<pre>fimo --verbosity 1 AATAAA.motif /Users/xuebing/Downloads/hotair-target.fa.fasta</pre>
<p>
    Settings:
    </p>
<pre><table>
<tr>
<td style="padding-right: 2em">output directory = fimo_out</td>
<td style="padding-left: 5em; padding-right: 2em">MEME file name = AATAAA.motif</td>
<td style="padding-left: 5em; padding-right: 2em">sequence file name = /Users/xuebing/Downloads/hotair-target.fa.fasta</td>
</tr>
<tr>
<td style="padding-right: 2em">background file name = (null)</td>
<td style="padding-left: 5em; padding-right: 2em">motif name = motif</td>
<td style="padding-left: 5em; padding-right: 2em">allow clobber = true</td>
</tr>
<tr>
<td style="padding-right: 2em">compute q-values = true</td>
<td style="padding-left: 5em; padding-right: 2em">output p-threshold set = false</td>
<td style="padding-left: 5em; padding-right: 2em">output q-threshold set = 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 sequence length = 250000000</td>
</tr>
<tr>
<td style="padding-right: 2em">output q-value threshold =   1</td>
<td style="padding-left: 5em; padding-right: 2em">output p-value threshold = 0.0001</td>
<td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
</tr>
<tr>
<td style="padding-right: 2em">verbosity = 1</td>
<td style="padding-left: 5em; padding-right: 2em"></td>
<td align="right"></td>
</tr>
</table></pre>
<p>
      This information can be useful in the event you wish to report a
      problem with the FIMO software.
    </p>
<hr>
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author	xuebing
date	Fri, 09 Mar 2012 19:37:19 -0500
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