<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>AED from MAKER in the based on nucleotide-level congruency of the transcript compared to the collapsed evidence.</div><div><br></div><div>eAED is also at the nucleotide level but is adjusted for inferred support of exons, such as can happen with mRNAseq (I.e. I can confirm the splice sites at each end but as the exon gets longer the middle is less likely to be covered). So if I can infer the middle based on ORF and the splice site are confirmed then I consider the middle of the exon to be confirmed for calculating eAED. eAED also adjusts for reading frame from protein evidence alignments, i.e. protein overlap in a different reading frame than the final gene model will not contribute to eAED. So because of this, eAED takes much longer to calculate but is sometimes more useful. Much of the time AED and eAED are identical.</div><div><br></div><div>Thanks,</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 Standage <<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 23 January, 2013 10:31 AM<br><span style="font-weight:bold">To: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Question about AED scores<br></div><div><br></div><div dir="ltr">Good morning!<div><br></div><div>I have a quick question or two about the AED scores reported for each transcript annotated by Maker. So, if I understand correctly, AED is 1-C, where the congruency C is the average of the sensitivity and specificity. The sn and sp values can be calculated for different levels (whole transcripts, exons, or individual nucleotides), but the text of the Maker2 paper suggests the reported AED value is calculated based on nucleotide-level congruency with the aligned evidence--is this correct?</div><div><br></div><div>I'm assuming this score is stored in the <b>_AED</b> attribute, which leads to my other question: what does the value of the <b>_eAED</b> attribute represent? Is this the same score calculated at the exon level?</div><div><br></div><div>Many thanks!<br clear="all"><div><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br></div></div></div>
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