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

Abstract

ABSTRACTMotivationTn-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.ResultsWe 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 ofde novodraft metabolic models. The utility of Tn-Core is demonstrated primarily using aSinorhizobium melilotimodel as a case study.Availability and implementationThe software can be downloaded fromhttps://github.com/diCenzo-GC/Tn-Core. All results presented in this work have been obtained with Tn-Core v. 1.0.Contactgeorgecolin.dicenzo@unifi.it,marco.fondi@unifi.itSupplementary informationSupplementary data are available at Bioinformatics online.