Translation table for miniprot?

[tseemann]

I see miniprot -T option is not used to set the translation table to the fungal schemes.

ODes this mean it is using the standard genetic code?

[nmquijada]

Hi @tseemann
Thank you for your comment.
ChroQueTas was trained with miniprot v0.12 (release in June 2023), that did not allow to select different genetic codes but the standard one. The -T flag in miniprot was released with their v0.13 in March this year.
Indeed, this is a very valuable point, and we are implementing this feature in ChroQueTas so the next version would allow to automatically select the genetic code to be used from standard (1) to the alternative yeast code (12) for the species within the CTG clade, based on the -s/--scheme flag.
We will push the release as soon as possible, together with schemes for 57 additional species and 210 proteins.
Best,
Narciso

[nmquijada]

Hi @tseemann

We have already released the new version of ChroQueTas that includes miniprot v>0.13 and thus their -T option (-c/--trans_code flag in ChroQueTas) for choosing the translation table.
Even the flag is susceptible for changing for the user, we set the automatic behaviour to:

• Alternative yeast code (12) for the species within the CTG clade
• Standard (1) for the other fungi

We strongly appreciate your suggestion, as we consider that it has greatly improved ChroQueTas.

Thanks a lot!
N