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

ABSTRACT Motivation Tn-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. Results We 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. Availability and implementation The 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. Contact [email protected] , [email protected] Supplementary information Supplementary data are available at Bioinformatics online.