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

[陈文博]

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: 内嵌图片 1]

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
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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