Question: How to extract gene names for a metabolic pathway from KEGG?
0
gravatar for becko
3.1 years ago by
becko0
becko0 wrote:

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 • 1.8k views
ADD COMMENTlink modified 3.1 years ago by lmanohara9920 • written 3.1 years ago by becko0

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.

ADD REPLYlink written 3.1 years ago by Pierre Lindenbaum131k
0
gravatar for EagleEye
3.1 years ago by
EagleEye6.7k
Sweden
EagleEye6.7k wrote:

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).

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by EagleEye6.7k
0
gravatar for lmanohara99
3.1 years ago by
lmanohara9920
Sri Lanka
lmanohara9920 wrote:

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.

ADD COMMENTlink written 3.1 years ago by lmanohara9920
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