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Article Dans Une Revue Bioinformatics Année : 2014

FindPath: a Matlab solution for in silico design of synthetic metabolic pathways

Résumé

A Summary: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files.
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Dates et versions

hal-01268971 , version 1 (28-05-2019)

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Gilles Vieira, Marc Carnicer Heras, Jean-Charles Portais, Stephanie Heux. FindPath: a Matlab solution for in silico design of synthetic metabolic pathways. Bioinformatics, 2014, 30 (20), pp.2986-2988. ⟨10.1093/bioinformatics/btu422⟩. ⟨hal-01268971⟩
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