Colocalization of enzyme by python
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19 months ago
trumbia ▴ 10

Hello,

I have several of NCBI ids of kinase enzyme and I would like to find their colocalization(nucleus or cytoplasm) by gene ontology(GO) in python.( it might be GOATOOLS). Do you recommend any library or tutorial for me via python since I am so confused? Do you have any example code for me? Thank you.

python gene ontology • 416 views
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I think if you download the goattool, they have several scripts and demos (based on this link)

https://pypi.org/project/goatools/

Other links that might help:

1) Sequence to EC number:

http://cansyl.metu.edu.tr/ECPred.html

2) EC number to GO ID

https://sourceforge.net/p/fun4me/code/ci/master/tree/data/ec2go

I think you need to find a tool that outputs the Cellular component given GO ID. I haven't used this tool but you can read its tutorial and see if it helps:

http://pantherdb.org/panther/ontologies.jsp?

GO has some tools that might help too:

http://geneontology.org/docs/tools-overview/

EC number to Pathway https://sourceforge.net/p/fun4me/code/ci/master/tree/data/ec2path

EC number info https://sourceforge.net/p/fun4me/code/ci/master/tree/data/enzyme.info

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