<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>eAED is a little more than that. It is still at a base pair level, but it uses exon inference from mRNAseq and in addition has a protein evidence overlap correction for each exon. Sometimes the overlapping protein reading frame doesn't perfectly match the entire model (exonerate for example can shift the reading frames by 1 in the middle to get a better alignment and BLAST can't). This means that just because you have physical overlap it may be meaningless overlap. eAED corrects for this. Also it can use inferred evidence from mRNAseq. For example if you have mRNAseq data that confirm both ends of an exon around the splice site, but not the middle of the exon, then there is probably enough correlated data for MAKER to confidently infer the middle of the exon. It then counts those base pairs as confirmed even though they don't physically overlap. This is common with mRNAseq data as it can taper off in the middle of long exons or won't align correctly around short exons. In both cases the middle gets left out. MAKER uses information from the reading frame and the ab initio predictors to infer if those regions.</div><div><br></div><div>Most of the time eAED and AED will be identical. eAED can sometimes be higher for certain mRNAseq alignments and lower for what are apparent spurious protein alignments.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, 21 December, 2012 12:08 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] AED eAED QI scores??<br></div><div><br></div><div dir="ltr"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><style type="text/css" id="owaParaStyle"></style><div 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> <a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a> [<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>] on behalf of Kapeel Chougule [<a href="mailto:kapeelc@gmail.com">kapeelc@gmail.com</a>]<br><b>Sent:</b> Thursday, December 20, 2012 4:00 PM<br><b>To:</b> <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><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></div></div>
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