<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>The gene model from maker is restricted to use the reading frame of the ab initio predictor. The better model would use a different reading frame. The augustus model has a missing exon so gets a lower score. Snap in general just looks bad. I'd say it needs to be retrained or maybe just drop Snap from the analysis.</div><div><br></div><div>--Carson<br><br>Sent from my iPhone</div><div><br>On Feb 9, 2015, at 7:06 PM, 陈文博 <<a href="mailto:chenwenbo1020@gmail.com">chenwenbo1020@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">Hi Daniel,<div><br></div><div>Thank you very much for suggestion.</div><div><br></div><div>I used three predictors, SNAP, Augustus and pred_gff. </div><div>From the image, I thought the prediction of Augustus(color is pink) matched the evidence better, why maker choose SNAP's ?</div><div><br></div><div><image.png><br></div><div><br></div><div>Thanks again</div><div>Best regards,</div><div>Wenbo</div></div><div class="gmail_extra"><br><div class="gmail_quote">2015-02-09 19:14 GMT-05:00 Daniel Ence <span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi, In the images that you sent, it looks like the ab-initio predictor had predicted two ORF’s, while the evidence supported a single model. MAKER doesn’t have an option to prefer longer models; it’s metric is to choose the prediction that is best supported by the alignment evidence.<br>
<br>
How many ab-initio predictors did you use in generating the results that you sent us? It looks like you only used one, which won’t give good results.<br>
<br>
~Daniel<br>
<span class=""><br>
<br>
> On Feb 9, 2015, at 4:20 PM, 陈文博 <<a href="mailto:chenwenbo1020@gmail.com">chenwenbo1020@gmail.com</a>> wrote:<br>
><br>
> Greetings,<br>
><br>
> I notices some cases in the output of Maker, that the ORF is not the longest one,<br>
> e.g. the one below<br>
</span>> <image.png><br>
<span class="">><br>
> If I manually correct it in Apollo as "calculate longes ORF", then it become<br>
</span>> <image.png><br>
<span class="">> I thought the updated one should make more sense. So how to let Maker output the longest ORF automatically?<br>
><br>
> Thanks very much!<br>
><br>
> Wenbo<br>
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