Gilles Vieira1, Marc Carnicer1, Jean-Charles Portais1, Stéphanie Heux1. 1. Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France and CNRS, UMR5504, F-31400 Toulouse, France Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France and CNRS, UMR5504, F-31400 Toulouse, France Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France and CNRS, UMR5504, F-31400 Toulouse, France.
Abstract
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.
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.
Authors: Pablo Carbonell; Andrew Currin; Adrian J Jervis; Nicholas J W Rattray; Neil Swainston; Cunyu Yan; Eriko Takano; Rainer Breitling Journal: Nat Prod Rep Date: 2016-05-17 Impact factor: 13.423