Question

How to translate EC number of enzymes in to corresponding Entrez gene ID?

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7.7 years ago

BioMed ▴ 50

Dear mate,

I have a question that need your assistance. How to translate EC number of enzymes in to corresponding Entrez gene ID in large scale (I have around 1000 candidates)?

I appreciate any suggestions.

enzyme genetics • 3.0k views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 7.7 years ago by BioMed ▴ 50

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From EC number to nucleotide sequence with biopython refers to getting sequence but you may be able to modify it if you only need ID's.

ADD REPLY • link 7.7 years ago by GenoMax 141k

score 1 · Answer 1 · 2016-08-10

You can try the mygene.info services.

Start from Gene info annotation service (http://mygene.info/v3/api#MyGene.info-gene-annotation-services ), and restrict fields to ec.

For example the following will get the e.c. of gene 384:

http://mygene.info/v3/gene/384?fields=ec%2Cname (arginase 2)

To automatize this for a large number of genes, have a look at the docs and the python APIs: http://docs.mygene.info/en/latest/doc/packages.html