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hyattpd / Prodigal

Prodigal Gene Prediction Software
GNU General Public License v3.0
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meta mode and translation table 4 #19

Closed tseemann closed 4 years ago

tseemann commented 8 years ago

Doug

Can you have a look at this Prodigal question/issue posted to Prokka?

https://github.com/tseemann/prokka/issues/112

davidbur commented 8 years ago

+1 When applying -p meta disregards -g xx. I tried -p meta -g 25 and stop codons were assigned for UGA codons.

Thanks.

ShaiberAlon commented 5 years ago

Hi,

Any plans on addressing this?

I run into a very similar problem to that @davidbur mentioned above: I try to use -p meta -g 25, and while UGA is not assigned to stop codon, it is translated to tryptophan (translation table 4) instead of glycine (translation table 25). If I use -p single -g 25 then UGA is translated to glycine properly.

Thank you!

hyattpd commented 4 years ago

This will be supported in the Go version (user will be able to specify which genetic codes of the pre-built models they want to use).

ShaiberAlon commented 4 years ago

Hi @hyattpd , thanks for following-up on this! What is the Go version?

hyattpd commented 4 years ago

New version that I am developing... I'll post more in the main README for Prodigal once it's closer to done.