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What are you trying to achieve? COGs are clusters. There are more API's than I can count. Please be more specific about what you would like to do, and where you might be stuck. You might find this guide to asking good questions helpful.
Hey, Thanks for that, I want to ask how to use the COG database for clustering. I have a set of protein sequences of bacteria and viruses and want to do functional annotation of those proteins, How can I use COG?
If your goal is functional classification (annotation) of protein sequences using the COG database, COGclassifier may be useful.