<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>If your organism is biased toward short genes with few introns, you might also want to try something like GeneMark. Not all gene predictors work well on all kinds of gene structures, so I often will run multiple and then drop those that perform poorly.</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> Sivaranjani Namasivayam <<a href="mailto:ranjani@uga.edu">ranjani@uga.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, 20 December, 2012 1:33 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> RE: [maker-devel] MAKER annotations<br></div><div><br></div><div dir="ltr"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><div ocsi="0" fpstyle="1" style="word-wrap:break-word; color:rgb(0,0,0); font-size:14px; font-family:Calibri,sans-serif"><div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">I am annotating a Apicomplexan organism. When I retrained I used both SNAP and Augustus. I will lower the AED score to 0.5 and check if that improves the results.<br>
Thanks for suggestion!<br><br>
Ranjani<br><div style="font-family: Times New Roman; color: #000000; font-size: 16px"><hr tabindex="-1"><div style="direction: ltr;" id="divRpF427209"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Carson Holt [<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>]<br><b>Sent:</b> Thursday, December 20, 2012 1:16 PM<br><b>To:</b> Sivaranjani Namasivayam; <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>Subject:</b> Re: [maker-devel] MAKER annotations<br></font><br></div><div></div><div><div>Don't use an AED filter of 0. It's too strict and will introduces certain artifacts like partial genes. Lower than 0.5 is probably sufficient for training. Also if in your first round you use Augustus, and the second round you used SNAP instead, you
may get poorer annotations because Augustus is performing better than SNAP. SNAP might need more training as well, especially if the low AED filter introduced partial gene artifacts. What kind of organism are you annotating?</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>Sivaranjani Namasivayam <<a href="mailto:ranjani@uga.edu" target="_blank">ranjani@uga.edu</a>><br><span style="font-weight:bold">Date: </span>Thursday, 20 December, 2012 12:21 PM<br><span style="font-weight:bold">To: </span>"<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span>[maker-devel] MAKER annotations<br></div><div><br></div><div dir="ltr"><style id="owaParaStyle" type="text/css">
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I have a query regarding MAKER predictions. I made a a first round of predictions with RNAseq data from 454 and Illumina as EST evidence and proteins sequences from related organisms as proteins evidence. I also used augustus trained on a closely related organism
as the ab-initio gene predictor.<br>
I got ~4000 maker annotations (I expect around ~10,000 genes)<br><br>
I used the annotations with AED score of 0 to train SNAP and used the HMM when retraining MAKER. This time I got ~8,000 genes but when I examined some annotations they appeared to be have worsened when compared to the initial predictions: that is, genes were
getting split, UTRs were not annotated and the original predictions were modified but not for better.
<br><br>
Would you have any suggestions on how I can improve the annotations.<br><br>
Also, is there a way to tell MAKER to produce gene models for all the cufflinks assembled transcripts(that is, for the data set I provide as EST evidence).<br><br>
Thanks,<br>
Ranjani<br></div></div></div>
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