[maker-devel] Incorrect translation start codon

[Carson Holt]

This is caused by BioPerl's is_start_codon method and default codon table
returning true for non-canonical start codons.  It was resolved some time
ago (See previous discussion -->
https://groups.google.com/forum/#!topic/maker-devel/S0j1fJ4LjVY ).  Make
sure you are using the most recent version of MAKER (currently 2.31).

Thanks,
Carson



https://groups.google.com/forum/#!topic/maker-devel/S0j1fJ4LjVY

On 3/25/14, 4:10 AM, "ernesto lowy gallego" <ernesto at ebi.ac.uk> wrote:

>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
>
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