Including CDS that overlaps with RNA

[adithi r v]

Hi,

I am running Prodigal on a bacterial genome and noticed that it eliminates genes that overlaps with an existing RNA. I am wondering if there is a way to stop Prodigal from excluding such cases because I would believe this is also common in prokaryotes.

Thanks in advance
Adithi

[Doug Hyatt]

Prodigal doesn't predict or do anything with RNA genes.  You may be thinking of Prokka or some other annotation system that combines Prodigal results with RNA genes predicted by another program, in which case the question should be addressed to the creators of those systems.

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