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Published 20 hours ago • verified publisher icon SysBioChalmers

Update with T2T-CHM13 genome

Open Yu-sysbio opened this issue 3 years ago • 3 comments

Hi, I am wondering if it is now possible to update the human GEM based on the new release of the human reference genome T2T-CHM13.

Yu-sysbio avatar Jul 14 '22 09:07 Yu-sysbio

Hi @Yu-sysbio, in general we retrieve our gene IDs and their associated symbols/other IDs from Ensembl. Is there something specific (gene/genes) that you're hoping to update?

JonathanRob avatar Jul 14 '22 14:07 JonathanRob

I am not interested in any specific genes but just found in the T2T-CHM13 paper that 99 newly introduced genes were predicted to be protein coding, which (if involved in metabolism) I think could be added to the human GEM. But I am not sure whether Ensembl has included the T2T-CHM13 genome.

Yu-sysbio avatar Jul 15 '22 08:07 Yu-sysbio

Ok interesting. Unless any of the newly added genes encode a protein that catalyzes a metabolic reaction, the update would not make a difference. Though if one of the new genes is associated with a reaction, then that reaction could be added to the model.

JonathanRob avatar Jul 18 '22 05:07 JonathanRob