Annotating bacterial intergenic regions

Question

[Gio]

Hello all,

I'd like to understand the function of a sequence which is in an intergenic region of a bacteria. Can you recommend programs to annotate these regions?

I'm conducting this on a diverse metagenome study.

Thank you

[michael.ante]

I don't know if I'm wrong with it, but most tools are for annotating genes and gene regions (e.g. prokka). If you run those and subtract (e.g. bedttols subtract) the genes from your contigs, you'll end up with the intergenic region.

[dthorbur]

Repeated elements might be worth looking at, tools like RepeatMasker/RepeatModeler would be a good place to start. Otherwise, maybe trying to find some ATAC-seq or ChIP-seq data you might see if it's implicated in regulation of transcription.