Posted a request for help on Twitter but I thought it might be of interest to some other people so am also posting about it here.
Basically what we (me and Lizzy Wilbanks in my lab) is to take some microbial genomes and to fully annotate all of the repeat elements and all of the possible mobile genetic elements in the genome. There are many reasons we want to do this but what we are struggling with right now is good informatics tools for doing it.
So if anyone has any suggestions for good computational methods for doing this it would be appreciated.
Below I have posted a “Storify” of the discussion in response to my question that has occurred on Twitter.