Abstract

Stoichiometric and constraint-based analyses of metabolic pathways have been gaining ground in the recent past with the increase in the quality and number of pathway databases available and the curation of genome-scale metabolic models. Genome-scale metabolic models of several organisms such as Escherichia coli , Saccharomyces cerevisiae and Staphylococcus aureus have already been constructed. Flux Balance Analysis (FBA) and Minimisation of Metabolic Adjustment (MoMA) are two of the popular techniques for the constraint-based analysis of metabolic pathways.We have developed a computational tool, PathwayAnalyser, for the analysis of metabolic pathways, particularly by FBA and MoMA. PathwayAnalyser interfaces with the open-source GNU Linear Programming Toolkit (GLPK) for linear programming/FBA and Object Oriented Quadratic Programming (OOQP) for quadratic programming/MoMA. It gives a comprehensive report on gene deletions from the Systems Biology Markup Language (SBML) Model and objective function input for FBA. PathwayAnalyser is open-source and is available at “http://sourceforge.net/projects/pathwayanalyser":http://sourceforge.net/projects/pathwayanalyser