<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" id="owaParaStyle"></style>
</head>
<body fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Kapeel, the QI columns are explained in the first maker paper (Cantarel and Yandell, Genome Research 2008).
<div><br>
</div>
<div>From pg. 189,</div>
<div>
<p class="p1">Table 2. Maker quality index summary</p>
<p class="p1">Length of the 5 UTR</p>
<p class="p1">Fraction of splice sites confirmed by an EST alignment</p>
<p class="p1">Fraction of exons that overlap an EST alignment</p>
<p class="p1">Fraction of exons that overlap EST or Protein alignments</p>
<p class="p1">Fraction of splice sites confirmed by a SNAP prediction</p>
<p class="p1">Fraction of exons that overlap a SNAP prediction</p>
<p class="p1">Number of exons in the mRNA</p>
<p class="p1">Length of the 3 UTR</p>
<p class="p1">Length of the protein sequence produced by the mRNA</p>
<p class="p1"><br>
</p>
<p class="p1">eAED is the the AED edit distance at an exon level, not base pair level like normal AED. </p>
<p class="p1"><br>
</p>
<p class="p1">Thanks,</p>
<p class="p1">Daniel </p>
<div><br>
<div class="BodyFragment"><font size="2">
<div class="PlainText">Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
</font></div>
</div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF763334" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> maker-devel-bounces@yandell-lab.org [maker-devel-bounces@yandell-lab.org] on behalf of Kapeel Chougule [kapeelc@gmail.com]<br>
<b>Sent:</b> Thursday, December 20, 2012 4:00 PM<br>
<b>To:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> [maker-devel] AED eAED QI scores??<br>
</font><br>
</div>
<div></div>
<div>Hello,
<div><br>
</div>
<div>I ran MAKER 2.27 using the option pred_stats=1 in the control file. In the last column of the maker output gff file I have the following annotation quality measures.</div>
<div><br>
</div>
<div>AED:0.41 eAED:0.41 QI:0|0.5|0.4|1|1|1|5|0|278</div>
<div><br>
</div>
<div>My understanding is that with AED score 0 your annotations are in prefect agreement with the evidence data sets and with AED 1,vice versa.</div>
<div><br>
</div>
<div> I would like to know what is the difference between AED against eAED score. And how do I interpret the QI cloumn?</div>
<div><br>
</div>
<div>Thank you,</div>
<div>
<div><br>
</div>
-- <br>
<font face="'courier new', monospace"><b>
<div><br>
</div>
<div>Kapeel Chougule</div>
<div>Systems Programmer</div>
<div>Arizona Genomics Institute (AGI)</div>
<div>Thomas W. Keating Bioresearch Building</div>
<div>University of Arizona</div>
<div>1657 E. Helen Street</div>
<div>Tucson, AZ 85719 </div>
<div><a href="http://www.genome.arizona.edu" target="_blank">www.genome.arizona.edu</a></div>
</b></font></div>
</div>
</div>
</div>
</div>
</body>
</html>