bio-systems-biology-metabolic-reconstruction

To build a genome-scale metabolic model from a protein FASTA file, this skill maps sequences to metabolic reactions using CarveMe or gapseq, applies gap-filling for defined media, and outputs draft SBML or JSON models.

Yes, you can construct merged community models for microbiome FBA by batch processing multiple bacterial or archaeal genomes to build individual reconstructions and merge them into a single community model.

Yes, this metabolic reconstruction workflow supports gap-filling for specific media like M9 or LB, ensuring the resulting genome-scale models are capable of simulating growth under those defined nutrient conditions.

You can inspect an SBML metabolic model and check for orphan reactions by loading the output with COBRApy, which reports reactions, metabolites, genes, and tests basic growth quality metrics.

The best way to automate draft metabolic reconstruction for bacterial and fungal genomes is using CarveMe or gapseq to map protein sequences to reactions, removing manual annotation and ad hoc gap-filling.

Both gapseq and CarveMe perform sequence alignment and reaction annotation to generate genome-scale models, but the choice depends on your specific bacterial, archaeal, or fungal genome inputs and desired gap-filling outcomes.