A question about GramPos/Neg template choose

cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction

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A question about GramPos/Neg template choose #127

Closed JY-97 closed 3 years ago

JY-97 commented 3 years ago

Hi Daniel, I am trying to use CarveMe to build GEMs based on the up-to-date RefSeq Assembly database. I have read your journal paper and wonder about the template choice for gram Neg or Pos bacteria. Is there a way to find reference for each Refseq Assambly accession number? How did you do that?

Many thanks!

JY-97 commented 3 years ago

We are using GEMs for some FBA analysis. So I am trying to make the new GEM consistent with the official released 5587 GEMs.

cdanielmachado commented 3 years ago

For the 5587 GEMs reconstruction we did not use gram positive or gram negative templates, we used the "default" universal bacterial model.