Comparison of genome-scale reconstructions using ModeRator

The Computational Intelligence is one of the main tools in biochemical network modeling that help predict or optimize engineering means of objectives to achieve. For this purpose, reconstructions (which tend to increase in number and size) of different genome-scale metabolic networks can be used. Consequently, realizing different tasks it is necessary to evaluate alternative models and to assess the quality, similarity and usefulness of the combination. This article provides an in depth look into reconstruction comparison software tool ModeRator for detection of inconsistencies, duplicate reactions and visualization of comparison results. A case study shows comparison results of two representative genome-scale metabolic network reconstructions containing 600 and 747 reactions. The obtained results show how using various options the threshold of comparison strictness can be lowered to reveal similar or probably equal reactions. The application, user manual and sample reconstructions can be downloaded from http://biosystems.lv/moderator2/. The ModeRator2 is implemented in Python and is freely available.