fetch out common/conserved genes from a bunch of bacteria species

Question

[zhangdengwei]

Hi all,

I have a difficulty in determining and fetching out the common/conserved regulator genes from a bunch of species. I fetched out all the regulator genes from each bacteria species according to the GFF annotation. I would like to determine which regulator gene is common/conserved across those bacteria species. Is there any approach to address this? Any suggestion would be greatly appreciated.

[Joe]

You could try an pangenome approach using a tool like roary. Once you get the list of core genes, parse out the regulators you are interested in. You can set various thresholds for presence and conservation to determine the level of preservation of the genes.

[zhangdengwei]

Thanks, Joe. I think it is an option for that. I have a quick look at roary that takes account into many aspects to compare genomes across species.