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<div><span></span><div>Dear sir:</div><div> After I finished my maker running, I should check the quality of my results.</div><div> My annotation purpose is to find some new proteins.</div><div> <span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">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;"> </span><b style="font-size: 10.5pt; line-height: 1.5; background-color: window;">how many predicted proteins can support the reviewed proteins</b><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">, how to do it?</span><b style="font-size: 10.5pt; line-height: 1.5; background-color: window;">(Can blastp be OK? How to set the threshold? )</b></div><div> I used Uniprot, ESTs and RNA-seq to do my annotation.<span style="font-size: 10.5pt; line-height: 1.5; background-color: window;"> 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). <b>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;"> </span></div><div><b style="font-size: 10.5pt; line-height: 1.5; background-color: window;"> </b></div><div> If not, maybe I can evaluate my proteins <span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">only</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;"> by AED value and</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;"> </span><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;">proteome domain?</span></div><div><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"><br></span></div><div> I'm looking forward to your help. Thanks a lot!</div><div><br></div><div>Yours sincerely!</div><div><br></div></div>
<div>Chao Chao</div><hr style="width: 210px; height: 1px;" color="#b5c4df" size="1" align="left">
<div><span><div style="MARGIN: 10px; FONT-FAMILY: verdana; FONT-SIZE: 10pt"><div>dcg@cau.edu.cn</div></div></span></div>
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