[Feature request] tRNA model for microeukaryotic/protist mitochondria

[jolespin]

Search Mode Options:

  -E                          : search for eukaryotic tRNAs (default)
  -B                          : search for bacterial tRNAs
  -A                          : search for archaeal tRNAs
  -M <model>                  : search for mitochondrial tRNAs
                                  options: mammal, vert
  -O                          : search for other organellar tRNAs
  -G                          : use general tRNA model (cytoslic tRNAs from all 3 domains included)
  --mt <model>                : use mito tRNA models for cytosolic/mito detemination
                                  (if not specified, only cytosolic isotype-specific model scan will be performed)

I'm trying to look at tRNA from protists and yeast mitochondria. What mito model would you recommend?

[patriciaplchan]

You can use the -O option. We currently do not have models specifically trained with mt-tRNAs in yeast or protists. So this generic organellar tRNA option is the best that can be used at this point.

[jolespin]

Perfect! That's what I set in the meantime. Glad I picked the best choice.

Would it be possible to add this functionality in the future?

[patriciaplchan]

Building models for detecting mt-tRNAs in yeast is one of the new features we have in our plan. Protist mt-tRNAs will not have as high priority though because many protists import at least a subset of cytosolic tRNAs into mitochondria instead of having them in the mitochondrial genomes, making it much harder to evaluate the completeness and accuracy of the detection. But we will note that as a user request.