retreiving genbank file of universal model

[acenieuw]

Hi,

I am currently in the process of comparing pipelines to construct metabolic models. In order to perform a fair benchmark, I want to export the universal model and the corresponding genbank file. I managed to retrieve the sbml file and a "genbank_release_221.tsv" file, but not a genbank file.

How can I get the genbank file of the universal model? Thanks in advance!

[cdanielmachado]

Could you be a bit more specific about what you mean with a genbank file of the universal model ?

[acenieuw]

Hi Daniel, thank you for your quick response!

So, I need a way to link the reaction Ids to GPRs which seem not to be present in the universal model (or the xml file of the model). I also need to link the gene ids to sequences. I thought I could do this via a genbank format file.

Though I am not an expert, I like the idea of CarveMe's underlying strategy of using a topdown approach because it allows for rapid model construction. It would be really awesome if I could include CarveMe in my benchmark project.

[cdanielmachado]

Thanks, that was much clearer now :)

You can find the GPR associations in this table:

https://github.com/cdanielmachado/carveme/blob/master/carveme/data/generated/bigg_gprs.csv.gz

And the amino acid sequences for all the BiGG genes are stored in this fasta file:

https://github.com/cdanielmachado/carveme/blob/master/carveme/data/input/bigg_proteins.faa

I hope this helps, and I look forward to seeing the results of your benchmark if you are allowed to share them.

[acenieuw]

Hi Daniel,

Thanks for the help! The benchmark is done with public data, so I will probably be able to share some of the results ;-)