Identifying core proteins -Pangenome
1
0
Entering edit mode
7.4 years ago
jackuser1979 ▴ 890

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?.

pangenome genomics coregenes coreproteins • 1.6k views
ADD COMMENT
0
Entering edit mode
7.4 years ago
dago ★ 2.8k

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1599 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