Identifying core proteins -Pangenome

Question

[jackuser1979]

I want to identify core proteins from pangenomic study. For this I used online tool Panseq(https://lfz.corefacility.ca/panseq/page/pan_full.html). In this tools, we have option to select full genomes of different strains,and it outputs result in coregenome fragments, and accessory genome fragments. In this I want to take coregenome fragments (usually in form of contigs) , and I need to convert them to proteins. Because my further study I will have to use core proteins. Can I do simple expsay translation (using standard code). Is the correct way to do this?.

Answer 1

[dago]

I am not familiar with the program you are using. But if the result of the analysis are contigs, I guess as a product of a whole genome alignment, I would say that in 99.9% of the case you will have multiple genes on them. Therefore you would need to do 2 things: gene calling and annotation(if needed). After that you will have the proteins sequences. You can use different tools for that for example prokka or RAST. Prokka needs some command line work, RAST is a clik and go web based tool.