[maker-devel] How to set "calculate longest ORF" in Maker

[Carson Holt]

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.

--Carson

Sent from my iPhone

> On Feb 9, 2015, at 7:06 PM, 陈文博 <chenwenbo1020 at gmail.com> wrote:
> 
> Hi Daniel,
> 
> Thank you very much for suggestion.
> 
> I used three predictors, SNAP, Augustus and pred_gff. 
> From the image, I thought the prediction of Augustus(color is pink) matched the evidence better, why maker choose SNAP's ?
> 
> <image.png>
> 
> Thanks again
> Best regards,
> Wenbo
> 
> 2015-02-09 19:14 GMT-05:00 Daniel Ence <dence at genetics.utah.edu>:
>> 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.
>> 
>> 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.
>> 
>> ~Daniel
>> 
>> 
>> > On Feb 9, 2015, at 4:20 PM, 陈文博 <chenwenbo1020 at gmail.com> wrote:
>> >
>> > Greetings,
>> >
>> > I notices some cases in the output of Maker, that the ORF is not the longest one,
>> > e.g. the one below
>> > <image.png>
>> >
>> > If I manually correct it in Apollo as "calculate longes ORF", then it become
>> > <image.png>
>> > I thought the updated one should make more sense. So how to let Maker output the longest ORF automatically?
>> >
>> > Thanks very much!
>> >
>> > Wenbo
>> > _______________________________________________
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>> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
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