<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Because of small differences in the assemblies, individual variants, annotated proteins used as reference being partial, as well as potential assembly error, a 100% identity expectation is too high. About 90+% would be more reasonable for a same species comparison. AED gives a good correlation with protein confidence. A perfect zero score will not happen often though since the way alignment algorithms work will leave alignment errors around splice sites and short exons. Also the evidence used is never perfect, so with AED lower values are better than higher values but can not be used as an overly specific measurement (it is only correlative and not exact).</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On May 5, 2017, at 7:43 AM, <a href="mailto:dcg@cau.edu.cn" class="">dcg@cau.edu.cn</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span class=""></span><div class="">Dear sir:</div><div class=""> After I finished my maker running, I should check the quality of my results.</div><div class=""> My annotation purpose is to find some new proteins.</div><div class=""> <span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">There is about 30K reviewed proteins of my species. If I want to see</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> </span><b style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">how many predicted proteins can support the reviewed proteins</b><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">, how to do it?</span><b style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">(Can blastp be OK? How to set the threshold? )</b></div><div class=""> I used Uniprot, ESTs and RNA-seq to do my annotation.<span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> From my perspective, if the protein is reviewed and used to train snap/augustus, we should get the same one after several training rounds. So I planned to align maker_proteins to Uniprot proteins(which I utilized to annotate).<span class="Apple-converted-space"> </span><b class="">If the predicted proteins match Uniprot by 100% identity and coverage, they can be thought to support the reviewed proteins. Is it correct?</b></span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> </span></div><div class=""><b style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> </b></div><div class=""> If not, maybe I can evaluate my proteins <span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">only</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> by AED value and</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> </span><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">proteome domain?</span></div><div class=""><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""><br class=""></span></div><div class=""> I'm looking forward to your help. Thanks a lot!</div><div class=""><br class=""></div><div class="">Yours sincerely!</div><div class=""><br class=""></div></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Chao Chao</div><hr size="1" align="left" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; width: 210px; height: 1px;" class=""><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span class=""><div style="margin: 10px; font-family: verdana; font-size: 10pt;" class=""><div class=""><a href="mailto:dcg@cau.edu.cn" class="">dcg@cau.edu.cn</a></div></div></span></div><span style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">maker-devel@box290.bluehost.com</a><br style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></body></html>