<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>I don’t know about Michaels’s script, but I’ve always used eval. It produces sensitivity/specificity metrics. It assumes the first models are 100% correct, and then tells you the sensitivity/specificity value for the second models.</div><div><br></div><div>It is not therefor a quality metric. Instead you should view it as a change metric. Lower sensitivity tells you that models/exons have been lost between versions, and lower specificity tells you models/exons have been gained. There will also be a lost of generic statistics on exon/intron distribution and UTR length. Then the AED values from the MAEKR run can be used independently to evaluate how well models match the evidence.</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> "Robert King (RRes-Roth)" <<a href="mailto:robert.king@rothamsted.ac.uk">robert.king@rothamsted.ac.uk</a>><br><span style="font-weight:bold">Date: </span> Monday, March 10, 2014 at 5:17 AM<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> [maker-devel] annotation comparison aed plots<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 14 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">Dear Maker Developers,<span class="apple-converted-space"> <o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;"><o:p> </o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">I’ve updated a reference that was had errors and was a little incomplete and now trying to produce a annotation
for it. Please note the reference has not changed dramatically. I’ve produced two annotations using as evidence:<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;"><o:p> </o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">Annotation 1:<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">Uniprot proteins search using species keyword “fusarium”<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">Pubmed mRNA for the name of the organism
<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">Prior annotation reference transcripts<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;"><o:p> </o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">Annotation 2:<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">Uniprot proteins search using species keyword “fusarium”<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">Pubmed mRNA for the name of the organism
<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">Prior annotation reference transcripts<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">mRNA trinity assembly pasafly of different strain (only RNA-seq available)<o:p></o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;"><o:p> </o:p></span></span></p><p class="MsoNormal"><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(34, 34, 34); background-color: white; background-position: initial initial; background-repeat: initial initial;">I’m not sure if it was a smart move to use the prior annotation reference transcripts?</span></span><o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">I want to compare these two annotations and have produced AED scores. How do I generate summary stats/figures to compare annotations. You mentioned last year in a post Mike Campbell has a script to produce these, do you know if he will
post it? I’ve got the Eval program and converted to gtf format using the provided script, just waiting on some perl modules to be installed by admin to test it. I’m waiting on some perl modules to be installed by our administrator to test out the “Evaluator”
and “compare” programs too, what do they do?<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">Best Wishes<o:p></o:p></p><p class="MsoNormal">Rob<o:p></o:p></p></div><br>--
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