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

ABSTRACT: Numerous methods exist to produce and refine genome-scale metabolic models. However, due to the use of incompatible identifier systems for metabolites and reactions, computing and visualizing the metabolic differences and similarities of such models is a current challenge. Furthermore, there is a lack of automated tools that can combine the strengths of multiple reconstruction pipelines into a curated single comprehensive model by merging different drafts, which possibly use incompatible namespaces. Here we present mergem, a novel method to compare, merge, and translate two or more metabolic models. Using a universal metabolic identifier mapping system constructed from multiple metabolic databases, mergem robustly can compare models from different pipelines, merge their commo

SUBMITTER: Hari A 

PROVIDER: S-EPMC10836943 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature