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linzhi2013 / MitoZ

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
https://doi.org/10.1093/nar/gkz173
GNU General Public License v3.0
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Use for plant mitochondria annotation #159

Open sanyalab opened 1 year ago

sanyalab commented 1 year ago

Hello,

Can this software be used to annotate plant mitochondria as well? If so, any tweaks required in the software? What are the drawbacks in calling plant mito genes.

Thanks Abhijit

linzhi2013 commented 1 year ago

Hi Abhijit,

thanks for your question!

MitoZ is designed for animal mitogenomes.

Have you tried https://dogma.ccbb.utexas.edu/ ?

sanyalab commented 1 year ago

Hello Lin,

I am aware that MitoZ is designed for animal mitogenomes. I am asking whether it has the capability of working on plant mitochondria as well. Do you see any pitfalls or drawbacks in doing this?

Thanks Abhijit

linzhi2013 commented 1 year ago

Hi Abhijit,

basically, many genes will be missing, as plant mitogenomes have different gene content compared to animal mitogenomes. For example, the rRNA CM models and tRNA profiles were trained with animal mitogenome data.

sanyalab commented 1 year ago

Hi Lin,

Thank you for the reply. Lets say for ncRNA and tRNA I use a seperate tool like infernal and tRNAscan-SE. For protein-coding gene prediction do you forsee any major issues? Like are you using models trained on animal protein-coding genes?

I only ask because I found your tool is easy to implement. Therefore, if I can tweak the gene models or prepare new ones, I can adapt this for plants.

Thanks Abhijit