Tn-Core: context-specific reconstruction of core metabolic models using Tn-seq data

MotivationTn-seq (transposon mutagenesis and sequencing) and constraint-based metabolic modelling represent highly complementary approaches. They can be used to probe the core genetic and metabolic networks underlying a biological process, revealing invaluable information for synthetic biology engineering of microbial cell factories. However, while algorithms exist for integration of -omics data sets with metabolic models, no method has been explicitly developed for integration of Tn-seq data with metabolic reconstructions.\n\nResultsWe report the development of Tn-Core, a Matlab toolbox designed to generate gene-centric, context-specific core reconstructions consistent with experimental Tn-seq data. Extensions of this algorithm allow: i) the generation of context-specific functional models through integration of both Tn-seq and RNA-seq data; ii) to visualize redundancy in core metabolic processes; and iii) to assist in curation of de novo draft metabolic models. The utility of Tn-Core is demonstrated primarily using a Sinorhizobium meliloti model as a case study.\n\nAvailability and implementationThe software can be downloaded from https://github.com/diCenzo-GC/Tn-Core. All results presented in this work have been obtained with Tn-Core v. 1.0.\n\nContactgeorgecolin.dicenzo@unifi.it, marco.fondi@unifi.it\n\nSupplementary informationSupplementary data are available at Bioinformatics online.