How to detect genomic clusters?

Question

[nancydong20]

Hello everyone!

I see a lot of genomics papers include schematics that show some genes of interest being physically clustered in a particular region of the genome. I would like to do similar analyses for my genome of interest. However, their methods don't provide details on how they did this. A search online for "genomic cluster" analysis didn't turn up anything either.

Does anyone know how these results came about?

Thank you very much!

[GenoMax]

Not sure what system you work with but in case of prokaryotes there is DOOR database. There is also a publication (cited on the site) that you can take a look at.

Answer 1

[Joe]

You mean schematics of operons? Depending on what exactly you want, I'd suggest SnapGene (if you want to do it 'by hand' with a great deal of customisation and ease), or EasyFig (usually used for alignments though), There's always the option of just making a screenshot of Artemis, JBrowse, IGV and any other genome viewer, if you have a genbank file. You'll need to give us a bit more to go on or an example figure you're trying to emulate before we can give you an exact answer.

And last (and definitely least), a lot of people I know, mainly less tech savvy PIs, will just draw it with boxes and arrows in powerpoint! (I absolutely do not endorse this :P )

[GenoMax]

I think OP is asking about actual discovery of genomic clusters not how to illustrate them.

[nancydong20]

Yes, I would like some suggestions on how to discover them given a new draft genome. I have some preliminary ideas from InterProScan results that there might be interesting physical clusters, but would like a more systematic way of analyzing them.

I am working with eukaryotes, unfortunately. :(