Mapping Gene Annotations to COG Classifications

Question

[ksipes]

I have a list of gene names that I got from Prokka annotations. I want to know the COG Categories of each of the annotated genes. I have a list of about 15,000 so a way to batch script this would be the best.

I'm thankful for any suggestions.

Answer 1

[Mensur Dlakic]

After Prokka installation, go to the db/hmm directory and either: 1) delete or temporarily move all databases except COGs; 2) rename the COG database so that its name is first alphanumerically (say, 1-COG). That way all your genes will have only COG annotation (case 1), or they will be first annotated according to COG database so that all possible COG annotations are included (case 2).

A somewhat relevant topic has been discussed recently.