fetch out common/conserved genes from a bunch of bacteria species
0
0
Entering edit mode
11 months ago
zhangdengwei ▴ 180

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.

common analysis genes comparative • 384 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 686 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6