Question about IS annotations

[avonm]

Hi,

I have recently used Prokka 1.14.0 re-annotating a couple of E. coli chromosomes with the hope to get the IS elements annotated (from the ISFinder database).

This works great, however I have one which and that is that the whole IS element is annotated and not only the CDS. For example, the IS element IS1X2 is 768 bp long containing a CDS (294 bp) encoding the transpose. In the end you would have a Mobile element annotation spanning the whole 768 bp as well as a CDS for the actual transpose.

Is that something that could be possible in future versions or maybe something you are already working towards.

Best,
Astrid

[tseemann]

I only annotate the tranposase because prokka is protein-based only.
Newer version of Prokka may one day support nucleotide databases.
You can use BLASTN yourself and create GFF lines from it and add to the Prokka GFF if you are able.
This is an open issue: #421