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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Mitochondrial mode for plants #17

Open sjackman opened 10 years ago

sjackman commented 10 years ago

prokka --kingdom mito sets the genetic code to metazoa mt (5) and enables the metazoan mitochondrial tRNA mode of Aragron aragorn -mt. Is -kingdom mito intended specifically for metazoa, or should it also work for plants?

https://github.com/Victorian-Bioinformatics-Consortium/prokka/blob/master/bin/prokka#L274

sjackman commented 10 years ago

What mode should RNAmmer and Barrnap be run in for a plant mitochondrion?

sjackman commented 10 years ago

The Cycas taitungensis mitochondrion has genes rrn5 rrn18 rrn26, so plant mitochondrion seem to need their own mode.

sjackman commented 10 years ago

I've created an issue for Barrnap to add support for plant mitochondrion: https://github.com/Victorian-Bioinformatics-Consortium/barrnap/issues/2

tseemann commented 9 years ago

@sjackman I think I'm chewing off more than I can bite with my attempt to add Mitochondria to Prokka's capabilities! They are more diverse than I first realised.