Comments (1)
Hi @coralzhang,
CarveMe is designed to transform a genome into a metabolic model. It expects a fasta file as input (preferably with AA sequences). So, if you can generate a fasta file (.faa) with all the proteins predicted by prokka/prodigal, you can give it to CarveMe to build a metabolic model.
However, you have to be careful with the interpretation of this model. Since you are providing metagenomics data with mixed species, the result will be a metabolic network with reactions from mixed species.
If you want to build one metabolic model per species, there are two options:
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Try to build complete metagenome assembled genomes (MAGs) from your metagenomics data. And then build one model for each MAG.
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Try to do taxonomic identification of your species and, if available, download the respective genomes from RefSeq.
If you try any of these options, let me know how it goes.
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