How to retrieve KO IDs for a list of genes?
2
0
Entering edit mode
10 months ago

Hi, community!!! I have downloaded a list of genes from the MetaCyc database for some bacterial species. I want to find out their respective KO IDs. Can anyone please tell me how can I do that?

Thanks

KEGG database • 603 views
ADD COMMENT
1
Entering edit mode
10 months ago
Mark ★ 1.1k

There are a lot of ways, but the easiest I have found is to use UniProt to match the genes to KO (or GO) ids. This is assuming your organism(s) are on uniprot and categorised.

Programmatically, you can use R package KEGGREST or Bio.KEGG in python.

ADD COMMENT
0
Entering edit mode

Thanks Mark!!! I have a large list. Can I retrieve the KO IDs as batch?

ADD REPLY
0
Entering edit mode

Yes, but the KEGG api limits how many you can send in a batch. I can't remember the limit but I think it was in the hundreds

ADD REPLY
0
Entering edit mode
10 months ago
xiaoguang ▴ 120

you can use uniprot https://www.uniprot.org/uploadlists/ Retrieve/ID mapping to get some KO columns. you can also use pir database https://proteininformationresource.org/

ADD COMMENT

Login before adding your answer.

Traffic: 1683 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