[maker-devel] Incorrect translation start codon

[ernesto lowy gallego]

Hi,

I have been inspecting the MAKER predictions and I detected a situation 
which appears with a certain frequency.
(See attached Apollo screenshot illustrating the situation I am going to 
describe):

Let's say that there is est2genome evidence supporting the prediction of 
the 5' UTR region, I have realized that in some of these transcripts 
with 5'UTR, MAKER is not capable of identifying the right downstream ATG 
protein start codon and considers a TTG codon (coding for L) as the 
incorrect protein start. The proper ATG codon start is further 
downstream, as the Ab-initio predictors (SNAP+AUGUSTUS) correctly 
predict in this case (see the attached screenshot)

Any comments on this?

Thanks!

ernesto

-- 
Developer

VectorBase | Ensembl Genomes

-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2014-03-25 at 09.34.16.png
Type: image/png
Size: 32220 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140325/f9ae69ec/attachment-0002.png>