Mercurial > repos > iuc > meme_psp_gen

<!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">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="UTF-8">
<title>FIMO Results</title>
<style type="text/css">
td.left {text-align: left;}
td.right {text-align: right; padding-right: 1cm;}
</head>
<body color="#000000">
<a name="top_buttons"></a>
<hr>
<table summary="buttons" align="left" cellspacing="0">
<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>
<td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td>
<td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td>
</tr>
</table>
<center><big><b>FIMO - Motif search tool</b></big></center>
FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700)
For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br>
To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>
<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.
<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
  Database contains 1 sequences, 16569 residues
         BEST POSSIBLE MATCH
Random model letter frequencies (--nrdb--):
A 0.275 C 0.225 G 0.225 T 0.275 </p>
<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
There were 11 motif occurences with a p-value less than 0.0001.
The full set of motif occurences can be seen in the
TSV (tab-delimited values) output file
The <i>p</i>-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.
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.
The q-value of a motif occurrence is defined as the
false discovery rate if the occurrence is accepted as significant.
<li>The table is sorted by increasing <i>p</i>-value.</li>
<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>
      <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>
</table>
<hr>
<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
This information can be useful in the event you wish to report a
problem with the FIMO software.
</body>
</html>
author	iuc
date	Sat, 27 Nov 2021 09:44:44 +0000
parents	ff2f53a32d0e
children	5f95d385a33c