How to extract gene names for a metabolic pathway from KEGG?
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3.6 years ago
becko • 0

I need the get the list of gene names involved in glycolysis (to put an example). Not manually, I need to do this in a script. Ideally with Python. I think KEGG is the proper database to do this, but any other (free) suggestion would do.

How can I do it?

python metabolism • 2.1k views
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Hello becko!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/2561

This is typically not recommended as it runs the risk of annoying people in both communities.

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3.6 years ago
EagleEye 6.8k

GeneSCF 'prepare_database' module will extract all the pathways with corresponding genes as simple table format in plain text file. Check 'Two step process' (sub-heading) from the provided link (First step will do your job).

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3.6 years ago
lmanohara99 ▴ 20

You can use KEGG REST API for extracting gene names from the pathway. Python request library can be used to make the REST calls to KEGG REST API and query information. Please follow this tutorial if you are a newbie to the Python programming and REST web services.

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