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

[Daniel Ence]

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