mergem: merging and comparing genome-scale metabolic models using universal identifiers

Abstract

AbstractNumerous methods exist to produce and refine draft genome-scale metabolic models. However, there is a lack of automated tools that can integrate these drafts into a curated single comprehensive model. In addition, computing and visualizing metabolic differences and similarities, including reconstructions using incompatible identifiers, is a current challenge. Here we presentmergem, a novel method to compare and merge two or more metabolic models using a universal metabolic identifier mapping system constructed from multiple metabolic databases.mergemis implemented as a Python package and on the web-application Fluxer, which allows simulating and comparing multiple models with different interactive flux graphs.