I'm looking for a way to identify low complexity regions and other repeats in the genome of Escherichia coli. I found that RepeatMasker may be used for example when drafting genomes of prokaryotes (E. coli example). But RepeatMasker works on a limited dataset of species, neither of them being prokaryotes. By default, when running RepeatMasker, if no species is specified, it will compare with homo sapiens data.
This seems rather inadequate, but the most relevent alternative, PRAP, requires a "dead" tool (VisCoSe, by Michael Spitzer).
- Is it still wise to to use RepeatMasker on Escherichia coli?
- If yes, which settings would maximise relevance ?