F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks

BMC Bioinformatics

Methodology Article

Abdelhalim Larhlimi¹  Joachim Selbig¹  Alexander Bockmayr²  Laszlo David³ 

[1] Department of Bioinformatics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam, Germany;Max-Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam, Germany;FB Mathematik und Informatik, Freie Universität Berlin, Arnimallee 6, D-14195, Berlin, Germany;DFG-Research Center Matheon, Arnimallee 6, D-14195, Berlin, Germany;FB Mathematik und Informatik, Freie Universität Berlin, Arnimallee 6, D-14195, Berlin, Germany;DFG-Research Center Matheon, Arnimallee 6, D-14195, Berlin, Germany;Berlin Mathematical School (BMS), Arnimallee 6, D-14195, Berlin, Germany;

关键词: Metabolic Network;    Couple Reaction;    Reversible Reaction;    Linear Programming Problem;    Coupling Relationship;   

DOI  :  10.1186/1471-2105-13-57

 received in 2011-12-16, accepted in 2012-02-23,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundFlux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state. On the one hand, this can help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions is in agreement with the experimental findings. On the other hand, FCA can aid in defining intervention strategies to knock out target reactions.ResultsWe present a new method F2C2 for FCA, which is orders of magnitude faster than previous approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed in a routine manner.ConclusionsWe propose F2C2 as a fast tool for the computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available for non-commercial use at https://sourceforge.net/projects/f2c2/files/.

【 授权许可】

CC BY   
© Larhlimi et al.; licensee BioMed Central Ltd. 2012