Using tRNAscan-SE for mitochondria tRNA from microeukaryotes like protists and yeast?

Question

[O.rka]

I'm working on calling tRNA genes from the mitochondria of protists and yeasts using tRNAscan-SE 2.x

Here's the search modes available:

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)

For mitochondria should I use -M vert, -O, or -B?

Answer 1

[shelkmike]

You should use -O.
-M and -B are for other taxons.