Methodology article
FFCA: a feasibility-based method for flux coupling analysis of metabolic networks
- † Equal contributors
1 DFG-Research Center Matheon, Berlin, Germany
2 FB Mathematik und Informatik, Freie Universität Berlin, Arnimallee 6, D-14195 Berlin, Germany
3 Berlin Mathematical School (BMS), Berlin, Germany
4 International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC), Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, D-14195 Berlin, Germany
5 Department of Bioinformatics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
6 School of Mathematics, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
BMC Bioinformatics 2011, 12:236 doi:10.1186/1471-2105-12-236
Published: 15 June 2011Abstract
Background
Flux coupling analysis (FCA) is a useful method for finding dependencies between fluxes of a metabolic network at steady-state. FCA classifies reactions into subsets (called coupled reaction sets) in which activity of one reaction implies activity of another reaction. Several approaches for FCA have been proposed in the literature.
Results
We introduce a new FCA algorithm, FFCA (Feasibility-based Flux Coupling Analysis), which is based on checking the feasibility of a system of linear inequalities. We show on a set of benchmarks that for genome-scale networks FFCA is faster than other existing FCA methods.
Conclusions
We present FFCA as a new method for flux coupling analysis and prove it to be faster than existing approaches. A corresponding software tool is freely available for non-commercial use at http://www.bioinformatics.org/ffca/ webcite.
