FindPath: a Matlab solution for in silico design of synthetic metabolic pathways.
basic_science · Level V
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- Record sourced from PubMed, PMID 24994891.
- Also identified by DOI 10.1093/bioinformatics/btu422.
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Abstract
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. http://metasys.insa-toulouse.fr/software/findpath/. heux@insa-toulouse.fr Supplementary data are available at Bioinformatics online.
Medical subject headings
- Computational Biology
- Computer Simulation
- Metabolic Networks and Pathways