Journal
GENOME BIOLOGY
Volume 22, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-021-02295-1
Keywords
Metabolic pathway analysis; Metabolic networks; Genome-scale metabolic models; Benchmark; Community simulation; Microbiome; Metagenome
Funding
- Deutsche Forschungsgemeinschaft [1182, 2167]
- German Ministry for Education and Research within the context of iTREAT (BMBF) [01ZX1902A]
- Projekt DEAL
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gapseq is a new tool that predicts metabolic pathways and automatically reconstructs microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. Based on scientific literature and experimental data, it outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilization, fermentation products, and metabolic interactions within microbial communities.
Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present gapseq (https://github.com/jotech/gapseq), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.
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