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

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

Research output: Indexed journal article Articlepeer-review

15 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)2986-2988
Number of pages3
JournalBioinformatics (Oxford, England)
Volume30
Issue number20
DOIs
Publication statusPublished - 15 Oct 2014
Externally publishedYes

Fingerprint

Dive into the research topics of 'FindPath: a Matlab solution for in silico design of synthetic metabolic pathways'. Together they form a unique fingerprint.

Cite this