Determine all "mobile DNAs" in an assembled bacteria genome (using something like Prokka)
I have been finding the Prokka software to be very useful annotating an assembled bacterial genome (contigs). I am trying to determine whether this assembled genome contains any "mobile DNAs" (and if so, how many, and their names). Is this something that can be interpreted easily from the Prokka output? And if not, are there any recommended software that can achieve this task?
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suzuBell •
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Specifically what mobile genetic elements are you after? Prokka does annotate insertion sequences but not sure about what else. The simplest solution is to grep gbk file for key words you're after.