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 ?
Is it wise to use RepeatMasker on prokaryotes?
genome;repeat elements;sequence analysis
If I understood correctly your question, you want to mask those regions in a (FASTA?) genome. I think you could identify those regions using mummer and mask them using bedtools.# align genome against itselfnucmer --maxmatch --nosimplify genome.fasta genome.fasta# select repeats and convert the corrdinates to bed formatshow-coords -r -T out.delta -H | awk '{if ($1 != $3 && $2 != $4) print $0}' | awk '{print $8\t$1\t$2}' > repeats.bed# mask those bases with bedtoolsbedtools maskfasta -fi genome.fasta -bed repeats.bed -fo masked.fastaHave a look at nucmer and bedtools maskfasta options to fine-tune your analysis.