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

Gilles Vieira, Marc Carnicer, Jean Charles Portais, Stéphanie Heux

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Resum

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.

AVAILABILITY AND IMPLEMENTATION: http://metasys.insa-toulouse.fr/software/findpath/.

CONTACT: heux@insa-toulouse.fr

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Idioma originalAnglès
Pàgines (de-a)2986-2988
Nombre de pàgines3
RevistaBioinformatics (Oxford, England)
Volum30
Número20
DOIs
Estat de la publicacióPublicada - 15 d’oct. 2014
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