Some questions about KO classification

SDPA_Pet · 09-06-2018, 08:37 PM

Hello, I have some questions about the KO classification.

I have a KO function abundance table. It will give me the basic level of KO funcitons ( the lowest level). Results like this:

#OTU ID Sample1

K01365 0
K01364 0
K01361 17
K01360 0
K01362 70832

KEGG database has higher levels of categories, which give me level 1, 2, 3.

For example I am interested in level 3, nitrogen metabolism category

I want to filter out all the KO functions related to nitrogen metablism

I want to create a table like this

#OTU ID Sample2
Nitrogen metabolism K0111 2
Nitrogen metabolism K0112 20
Nitrogen metabolism K0112 3000

This will help me to extract the functions that I am interested in. Anyone knows how to do this? -- extract all functions related to a category.

Also, I want to know the gene name of the KO funcitons.

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09-06-2018, 08:37 PM	#1
SDPA_Pet Senior Member Location: US Join Date: Apr 2013 Posts: 222	Some questions about KO classification Hello, I have some questions about the KO classification. I have a KO function abundance table. It will give me the basic level of KO funcitons ( the lowest level). Results like this: #OTU ID Sample1 K01365 0 K01364 0 K01361 17 K01360 0 K01362 70832 KEGG database has higher levels of categories, which give me level 1, 2, 3. For example I am interested in level 3, nitrogen metabolism category I want to filter out all the KO functions related to nitrogen metablism I want to create a table like this #OTU ID Sample2 Nitrogen metabolism K0111 2 Nitrogen metabolism K0112 20 Nitrogen metabolism K0112 3000 This will help me to extract the functions that I am interested in. Anyone knows how to do this? -- extract all functions related to a category. Also, I want to know the gene name of the KO funcitons.