84 lines
3.9 KiB
HTML
Executable File
84 lines
3.9 KiB
HTML
Executable File
<!DOCTYPE html>
|
|
<html>
|
|
<head>
|
|
<meta charset="utf-8">
|
|
<title>DREME Tutorial - MEME Suite</title>
|
|
<link rel="shortcut icon" type="image/x-icon" href="images/memesuite_icon.ico">
|
|
<link rel="icon" type="image/png" href="images/memesuite_icon.png">
|
|
<link href="css/style.css" rel="stylesheet" type="text/css">
|
|
<script src="js/menu.js"></script>
|
|
</head>
|
|
<body>
|
|
<div class="memesuitelogo">
|
|
<h1>The MEME Suite</h1>
|
|
<h2>Motif-based sequence analysis tools</h2>
|
|
</div>
|
|
<h2>DREME Tutorial</h2>
|
|
<h3>Overview</h3>
|
|
<p>DREME is a tool for discovering short regular expression motifs that
|
|
are enriched in the provided dataset. It is limited to working with DNA or RNA
|
|
as the large combination space for amino acids makes DREME's approach
|
|
unfeasible. DREME also has the capability of using two datasets to
|
|
find motifs that are enriched in one when compared to the other.
|
|
<h3>How DREME works</h3>
|
|
<p>Note the following refers to the sequence set in which you are finding
|
|
motifs as the positive sequences and to the control sequence
|
|
set as the negative sequences.
|
|
<ol>
|
|
<li>If there are no negative sequences provided then di-nucleotide
|
|
shuffle the positive sequences to create one.</li>
|
|
<li>Count the number of positive sequences and the number of negative
|
|
sequences.</li>
|
|
<li>Find all unique subsequences with no ambiguity characters that
|
|
have a length in the range given (3 to 8 nucleotides by default)
|
|
in the positive sequences.</li>
|
|
<li>For each of the subsequences
|
|
<ol>
|
|
<li>Count the number of sequences it occurs in for the positive and
|
|
negative sequences.</li>
|
|
<li>Use Fisher's exact test to determine the significance.</li>
|
|
<li>Add the subsequence to a sorted (by <i>p</i>-value) set of regular
|
|
expression motifs.</li>
|
|
</ol>
|
|
</li>
|
|
<li>Repeatedly pick the top motifs (default 100) to generalize
|
|
by replacing one position with each possible ambiguity code and
|
|
estimating the resultant <i>p</i>-value. This is done enough times to allow
|
|
each position to have an ambiguity code.</li>
|
|
<li>For each of the top (default 100) generalized RE motifs
|
|
<ol>
|
|
<li>Count the number of sequences matched in the positive and negative
|
|
sequences.</li>
|
|
<li>Use Fisher's exact test to determine the significance.</li>
|
|
</ol>
|
|
</li>
|
|
<li>Pick the best RE motif and (assuming it meets the <i>E</i>-value threshold)
|
|
scan for all matching sites to build up a frequency matrix and report
|
|
it.</li>
|
|
<li>Mask the matched sites with the wildcard character 'N'.</li>
|
|
<li>If the limits have not been met then loop back to step 3 to find
|
|
more motifs.</li>
|
|
</ol>
|
|
<h3>Sequence set</h3>
|
|
<p>DREME works best with lots of short (~100bp) sequences. If you have a
|
|
couple of long sequences then it might be beneficial to split them into
|
|
many smaller (~100bp) sequences. With ChIP-seq data we recommend using
|
|
100bp regions around the peaks.</p>
|
|
<h3>Comparative sequence set</h3>
|
|
<p>DREME always uses a control sequence set but you don't have to supply
|
|
it as DREME can create it by using di-nucleotide shuffling. If you wish
|
|
to use your own sequence set then there are a few guidelines you should
|
|
follow.</p>
|
|
|
|
<p>The sequence lengths of the control sequences should be roughly
|
|
the same as the sequences to search for motifs. This is because the null
|
|
model assumes that the probability of finding a match in a sequence in
|
|
either sequence set will be roughly the same for an uninteresting motif.
|
|
If the control sequences are longer this provides more
|
|
locations that the motif could match making it more likely it will match
|
|
and hence skewing the <i>p</i>-value calculations, possibly
|
|
excluding a motif you would be interested in.</p>
|
|
</body>
|
|
</html>
|
|
|